Starting phenix.real_space_refine on Mon Jul 6 09:52:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v88_43030/07_2026/8v88_43030_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v88_43030/07_2026/8v88_43030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v88_43030/07_2026/8v88_43030_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v88_43030/07_2026/8v88_43030_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v88_43030/07_2026/8v88_43030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v88_43030/07_2026/8v88_43030.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 9 Type Number sf(0) Gaussians Ca 5 9.91 5 Br 5 7.06 5 P 10 5.49 5 S 120 5.16 5 Cl 5 4.86 5 C 11330 2.51 5 N 2640 2.21 5 O 3210 1.98 5 H 15865 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33190 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6367 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 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, 6343 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: 6401 Chain: "B" Number of atoms: 6367 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 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, 6343 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: 6401 Chain: "C" Number of atoms: 6367 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 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, 6343 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: 6401 Chain: "D" Number of atoms: 6367 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 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, 6343 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: 6401 Chain: "E" Number of atoms: 6367 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 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, 6343 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: 6401 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 230 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 3, 'YLI': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 183 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 183 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 183 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 136 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 1, 'YLI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Time building chain proxies: 9.69, per 1000 atoms: 0.29 Number of scatterers: 33190 At special positions: 0 Unit cell: (100.347, 101.426, 166.166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Br 5 34.99 Ca 5 19.99 Cl 5 17.00 S 120 16.00 P 10 15.00 O 3210 8.00 N 2640 7.00 C 11330 6.00 H 15865 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 G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 502 " - " ASN A 67 " " NAG B 502 " - " ASN B 67 " " NAG C 502 " - " ASN C 67 " " NAG D 502 " - " ASN D 67 " " NAG E 502 " - " ASN E 67 " " NAG F 1 " - " ASN A 23 " " NAG G 1 " - " ASN A 110 " " NAG H 1 " - " ASN B 23 " " NAG I 1 " - " ASN B 110 " " NAG J 1 " - " ASN C 23 " " NAG K 1 " - " ASN C 110 " " NAG L 1 " - " ASN D 23 " " NAG M 1 " - " ASN D 110 " " NAG N 1 " - " ASN E 23 " " NAG O 1 " - " ASN E 110 " Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.6 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 44.7% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.504A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.520A pdb=" N CYS A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.636A pdb=" N THR A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE A 252 " --> pdb=" O SER A 248 " (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 465 Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.503A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.520A pdb=" N CYS B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.636A pdb=" N THR B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (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 465 Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.504A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 214 through 226 removed outlier: 3.520A pdb=" N CYS C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 231 Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.636A pdb=" N THR C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE C 252 " --> pdb=" O SER C 248 " (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 465 Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.503A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 214 Processing helix chain 'D' and resid 214 through 226 removed outlier: 3.520A pdb=" N CYS D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 231 Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 237 through 260 removed outlier: 3.636A pdb=" N THR D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE D 252 " --> pdb=" O SER D 248 " (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 465 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.503A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'E' and resid 214 through 226 removed outlier: 3.520A pdb=" N CYS E 218 " --> pdb=" O LEU E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 231 Processing helix chain 'E' and resid 232 through 236 Processing helix chain 'E' and resid 237 through 260 removed outlier: 3.636A pdb=" N THR E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE E 252 " --> pdb=" O SER E 248 " (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 465 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: 4.032A 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: 4.032A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN A 52 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE A 39 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N TRP A 54 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU A 37 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLN A 56 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N SER A 35 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N SER A 58 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N SER A 33 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N THR A 60 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N TYR A 31 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.256A 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: 4.580A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.602A 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 removed outlier: 4.580A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU A 192 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR A 187 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.032A 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: 4.032A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN B 52 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE B 39 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N TRP B 54 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU B 37 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLN B 56 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N SER B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N SER B 58 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N SER B 33 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N THR B 60 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 9.701A pdb=" N TYR B 31 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.256A 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: 4.581A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.602A 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 removed outlier: 4.581A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU B 192 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR B 187 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.032A 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: 4.032A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN C 52 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE C 39 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N TRP C 54 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU C 37 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLN C 56 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N SER C 35 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N SER C 58 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N SER C 33 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N THR C 60 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N TYR C 31 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.257A 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: 4.580A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.602A 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 removed outlier: 4.580A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU C 192 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR C 187 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.032A 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: 4.032A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLN D 56 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N SER D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N SER D 58 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N SER D 33 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N THR D 60 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N TYR D 31 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.257A 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: 4.580A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.602A 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 removed outlier: 4.580A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU D 192 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR D 187 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.032A 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: 4.032A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN E 52 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE E 39 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N TRP E 54 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU E 37 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLN E 56 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N SER E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N SER E 58 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N SER E 33 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N THR E 60 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N TYR E 31 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.256A 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: 4.581A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.603A 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 removed outlier: 4.581A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLU E 192 " --> pdb=" O TYR E 187 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR E 187 " --> pdb=" O GLU E 192 " (cutoff:3.500A) 951 hydrogen bonds defined for protein. 2748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.55 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 15835 1.05 - 1.26: 2610 1.26 - 1.47: 7223 1.47 - 1.69: 7737 1.69 - 1.90: 185 Bond restraints: 33590 Sorted by residual: bond pdb=" NZ LYS D 303 " pdb=" HZ2 LYS D 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 B 412 " pdb=" HZ2 LYS B 412 " 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 323 " pdb=" HZ2 LYS B 323 " 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 D 238 " pdb=" HZ2 LYS D 238 " 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 E 306 " pdb=" HZ1 LYS E 306 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 33585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 56011 2.44 - 4.88: 4045 4.88 - 7.32: 138 7.32 - 9.76: 16 9.76 - 12.20: 10 Bond angle restraints: 60220 Sorted by residual: angle pdb=" O11 POV B 503 " pdb=" P POV B 503 " pdb=" O12 POV B 503 " ideal model delta sigma weight residual 97.67 109.87 -12.20 3.00e+00 1.11e-01 1.65e+01 angle pdb=" O11 POV E 503 " pdb=" P POV E 503 " pdb=" O12 POV E 503 " ideal model delta sigma weight residual 97.67 109.85 -12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" O11 POV D 503 " pdb=" P POV D 503 " pdb=" O12 POV D 503 " ideal model delta sigma weight residual 97.67 109.83 -12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O11 POV A 503 " pdb=" P POV A 503 " pdb=" O12 POV A 503 " ideal model delta sigma weight residual 97.67 109.83 -12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O11 POV C 503 " pdb=" P POV C 503 " pdb=" O12 POV C 503 " ideal model delta sigma weight residual 97.67 109.82 -12.15 3.00e+00 1.11e-01 1.64e+01 ... (remaining 60215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.64: 16357 31.64 - 63.29: 548 63.29 - 94.93: 100 94.93 - 126.58: 30 126.58 - 158.22: 10 Dihedral angle restraints: 17045 sinusoidal: 9850 harmonic: 7195 Sorted by residual: dihedral pdb=" CA CYS E 189 " pdb=" C CYS E 189 " pdb=" N CYS E 190 " pdb=" CA CYS E 190 " ideal model delta harmonic sigma weight residual 180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 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 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA CYS D 189 " pdb=" C CYS D 189 " pdb=" N CYS D 190 " pdb=" CA CYS D 190 " ideal model delta harmonic sigma weight residual -180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 17042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2271 0.056 - 0.112: 376 0.112 - 0.169: 75 0.169 - 0.225: 15 0.225 - 0.281: 18 Chirality restraints: 2755 Sorted by residual: chirality pdb=" C3 EPJ A 506 " pdb=" C2 EPJ A 506 " pdb=" C4 EPJ A 506 " pdb=" N1 EPJ A 506 " both_signs ideal model delta sigma weight residual False 3.28 3.00 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C3 EPJ B 506 " pdb=" C2 EPJ B 506 " pdb=" C4 EPJ B 506 " pdb=" N1 EPJ B 506 " both_signs ideal model delta sigma weight residual False 3.28 3.00 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C3 EPJ C 506 " pdb=" C2 EPJ C 506 " pdb=" C4 EPJ C 506 " pdb=" N1 EPJ C 506 " both_signs ideal model delta sigma weight residual False 3.28 3.00 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2752 not shown) Planarity restraints: 4745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " -0.079 2.00e-02 2.50e+03 6.68e-02 5.58e+01 pdb=" C7 NAG C 502 " 0.017 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " 0.020 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " 0.106 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 502 " 0.079 2.00e-02 2.50e+03 6.67e-02 5.56e+01 pdb=" C7 NAG B 502 " -0.017 2.00e-02 2.50e+03 pdb=" C8 NAG B 502 " -0.020 2.00e-02 2.50e+03 pdb=" N2 NAG B 502 " -0.106 2.00e-02 2.50e+03 pdb=" O7 NAG B 502 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 502 " -0.079 2.00e-02 2.50e+03 6.67e-02 5.56e+01 pdb=" C7 NAG D 502 " 0.017 2.00e-02 2.50e+03 pdb=" C8 NAG D 502 " 0.020 2.00e-02 2.50e+03 pdb=" N2 NAG D 502 " 0.106 2.00e-02 2.50e+03 pdb=" O7 NAG D 502 " -0.064 2.00e-02 2.50e+03 ... (remaining 4742 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.22: 2284 2.22 - 2.84: 73412 2.84 - 3.46: 89738 3.46 - 4.08: 138630 4.08 - 4.70: 208397 Nonbonded interactions: 512461 Sorted by model distance: nonbonded pdb=" HZ1 LYS B 144 " pdb=" HH TYR B 187 " model vdw 1.606 2.100 nonbonded pdb=" HZ1 LYS C 144 " pdb=" HH TYR C 187 " model vdw 1.606 2.100 nonbonded pdb=" HZ1 LYS A 144 " pdb=" HH TYR A 187 " model vdw 1.607 2.100 nonbonded pdb=" HZ1 LYS E 144 " pdb=" HH TYR E 187 " model vdw 1.607 2.100 nonbonded pdb=" HZ1 LYS D 144 " pdb=" HH TYR D 187 " model vdw 1.607 2.100 ... (remaining 512456 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 503)) selection = (chain 'B' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 503)) selection = (chain 'C' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 503)) selection = (chain 'D' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 503)) selection = (chain 'E' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 503)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.230 Extract box with map and model: 0.410 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 37.740 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.006 0.064 17755 Z= 0.319 Angle : 0.833 12.195 24235 Z= 0.383 Chirality : 0.050 0.281 2755 Planarity : 0.006 0.067 2860 Dihedral : 18.065 158.219 7650 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.17), residues: 1960 helix: -0.37 (0.16), residues: 815 sheet: -0.63 (0.22), residues: 445 loop : -0.14 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG C 425 TYR 0.015 0.002 TYR D 273 PHE 0.019 0.002 PHE E 99 TRP 0.008 0.001 TRP C 133 HIS 0.004 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.32 (17715) covalent geometry : angle 0.82083 / 0.38 (24125) SS BOND : bond 0.00764 / 0.42 ( 10) SS BOND : angle 1.72415 / 1.08 ( 20) hydrogen bonds : bond 0.19838 / 12.81 ( 846) hydrogen bonds : angle 6.95813 / 4.86 ( 2748) link_BETA1-4 : bond 0.00328 / 0.18 ( 15) link_BETA1-4 : angle 1.83529 / 1.21 ( 45) link_NAG-ASN : bond 0.00253 / 0.13 ( 15) link_NAG-ASN : angle 2.71576 / 1.71 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8039 (mp) cc_final: 0.7760 (tp) REVERT: B 159 MET cc_start: 0.8546 (ttp) cc_final: 0.8274 (ttp) REVERT: B 446 ARG cc_start: 0.8419 (tpp80) cc_final: 0.8162 (tpp80) REVERT: C 57 MET cc_start: 0.8991 (mtm) cc_final: 0.8737 (mtm) REVERT: C 128 TYR cc_start: 0.8746 (t80) cc_final: 0.8486 (t80) REVERT: C 188 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6470 (mt-10) REVERT: C 210 TYR cc_start: 0.8544 (m-80) cc_final: 0.8255 (m-80) REVERT: D 159 MET cc_start: 0.8491 (ttp) cc_final: 0.8272 (ttp) REVERT: D 188 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6600 (mt-10) REVERT: E 159 MET cc_start: 0.8516 (ttp) cc_final: 0.8297 (ttp) REVERT: E 170 ASN cc_start: 0.7685 (t0) cc_final: 0.7411 (t0) REVERT: E 253 MET cc_start: 0.8912 (ttp) cc_final: 0.8691 (ttp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 1.4040 time to fit residues: 358.6902 Evaluate side-chains 199 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.129862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.097882 restraints weight = 55397.478| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.62 r_work: 0.2884 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17755 Z= 0.134 Angle : 0.588 5.358 24235 Z= 0.295 Chirality : 0.041 0.147 2755 Planarity : 0.004 0.041 2860 Dihedral : 16.141 149.659 3870 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.78 % Allowed : 5.36 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.18), residues: 1960 helix: 1.50 (0.17), residues: 815 sheet: -0.29 (0.23), residues: 445 loop : 0.08 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 446 TYR 0.009 0.001 TYR E 14 PHE 0.011 0.001 PHE A 99 TRP 0.007 0.001 TRP D 153 HIS 0.002 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (17715) covalent geometry : angle 0.57322 / 0.29 (24125) SS BOND : bond 0.00812 / 0.44 ( 10) SS BOND : angle 1.56673 / 0.96 ( 20) hydrogen bonds : bond 0.06297 / 4.07 ( 846) hydrogen bonds : angle 5.07079 / 3.55 ( 2748) link_BETA1-4 : bond 0.00297 / 0.16 ( 15) link_BETA1-4 : angle 1.89056 / 1.34 ( 45) link_NAG-ASN : bond 0.00146 / 0.08 ( 15) link_NAG-ASN : angle 2.35580 / 1.51 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.898 Fit side-chains REVERT: B 159 MET cc_start: 0.8952 (ttp) cc_final: 0.8725 (ttp) REVERT: B 196 ASP cc_start: 0.8906 (p0) cc_final: 0.8633 (p0) REVERT: B 446 ARG cc_start: 0.8638 (tpp80) cc_final: 0.8414 (tpp80) REVERT: C 170 ASN cc_start: 0.7742 (t0) cc_final: 0.7531 (t0) REVERT: C 210 TYR cc_start: 0.8668 (m-80) cc_final: 0.8298 (m-80) REVERT: C 431 GLU cc_start: 0.7777 (pp20) cc_final: 0.7368 (pt0) REVERT: D 163 ASP cc_start: 0.8837 (t70) cc_final: 0.8582 (t70) REVERT: D 260 MET cc_start: 0.8625 (mmp) cc_final: 0.8363 (mmp) REVERT: E 170 ASN cc_start: 0.7649 (t0) cc_final: 0.7412 (t0) outliers start: 14 outliers final: 7 residues processed: 217 average time/residue: 1.3990 time to fit residues: 338.9198 Evaluate side-chains 206 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 199 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 475 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 34 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 16 optimal weight: 0.0010 chunk 112 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.097155 restraints weight = 51943.352| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.52 r_work: 0.2870 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17755 Z= 0.134 Angle : 0.558 7.462 24235 Z= 0.280 Chirality : 0.040 0.150 2755 Planarity : 0.004 0.036 2860 Dihedral : 14.067 128.849 3870 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.61 % Allowed : 6.15 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.18), residues: 1960 helix: 1.99 (0.17), residues: 815 sheet: -0.25 (0.22), residues: 445 loop : 0.17 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 446 TYR 0.014 0.001 TYR E 14 PHE 0.015 0.001 PHE A 99 TRP 0.008 0.001 TRP C 59 HIS 0.003 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (17715) covalent geometry : angle 0.54204 / 0.28 (24125) SS BOND : bond 0.00807 / 0.44 ( 10) SS BOND : angle 1.62147 / 0.99 ( 20) hydrogen bonds : bond 0.05788 / 3.74 ( 846) hydrogen bonds : angle 4.81289 / 3.37 ( 2748) link_BETA1-4 : bond 0.00405 / 0.23 ( 15) link_BETA1-4 : angle 1.73899 / 1.22 ( 45) link_NAG-ASN : bond 0.00120 / 0.07 ( 15) link_NAG-ASN : angle 2.40863 / 1.54 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 210 time to evaluate : 0.911 Fit side-chains REVERT: A 247 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7428 (tp) REVERT: B 159 MET cc_start: 0.8973 (ttp) cc_final: 0.8696 (ttp) REVERT: B 196 ASP cc_start: 0.8923 (p0) cc_final: 0.8653 (p0) REVERT: C 170 ASN cc_start: 0.7831 (t0) cc_final: 0.7614 (t0) REVERT: C 191 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8138 (mmtt) REVERT: C 431 GLU cc_start: 0.7696 (pp20) cc_final: 0.7294 (pt0) REVERT: C 446 ARG cc_start: 0.8536 (tpp80) cc_final: 0.8281 (tpp80) REVERT: D 40 MET cc_start: 0.8613 (mtp) cc_final: 0.8326 (mtp) REVERT: D 210 TYR cc_start: 0.8688 (m-80) cc_final: 0.8292 (m-80) REVERT: D 446 ARG cc_start: 0.8582 (tpp80) cc_final: 0.8256 (tpp80) REVERT: E 445 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7551 (t0) outliers start: 11 outliers final: 4 residues processed: 212 average time/residue: 1.4044 time to fit residues: 332.3217 Evaluate side-chains 208 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 202 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 475 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.126408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.095007 restraints weight = 51085.876| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.50 r_work: 0.2833 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17755 Z= 0.195 Angle : 0.609 6.820 24235 Z= 0.311 Chirality : 0.042 0.171 2755 Planarity : 0.005 0.038 2860 Dihedral : 12.874 113.010 3870 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.84 % Allowed : 6.54 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.18), residues: 1960 helix: 1.98 (0.17), residues: 815 sheet: -0.36 (0.22), residues: 435 loop : 0.13 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 446 TYR 0.016 0.002 TYR D 14 PHE 0.023 0.002 PHE D 99 TRP 0.010 0.002 TRP C 148 HIS 0.004 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (17715) covalent geometry : angle 0.59240 / 0.31 (24125) SS BOND : bond 0.00839 / 0.45 ( 10) SS BOND : angle 1.98618 / 1.21 ( 20) hydrogen bonds : bond 0.06237 / 4.03 ( 846) hydrogen bonds : angle 4.91346 / 3.44 ( 2748) link_BETA1-4 : bond 0.00312 / 0.17 ( 15) link_BETA1-4 : angle 1.72353 / 1.21 ( 45) link_NAG-ASN : bond 0.00164 / 0.08 ( 15) link_NAG-ASN : angle 2.62180 / 1.66 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.9006 (ttp) cc_final: 0.8682 (ttp) REVERT: B 196 ASP cc_start: 0.8950 (p0) cc_final: 0.8667 (p0) REVERT: C 128 TYR cc_start: 0.8797 (t80) cc_final: 0.8520 (t80) REVERT: C 191 LYS cc_start: 0.8371 (mmtt) cc_final: 0.8139 (mmtt) REVERT: C 431 GLU cc_start: 0.7714 (pp20) cc_final: 0.7307 (pt0) REVERT: C 446 ARG cc_start: 0.8553 (tpp80) cc_final: 0.8295 (tpp80) REVERT: D 40 MET cc_start: 0.8661 (mtp) cc_final: 0.8372 (mtp) REVERT: D 210 TYR cc_start: 0.8630 (m-80) cc_final: 0.8310 (m-80) REVERT: E 196 ASP cc_start: 0.8911 (p0) cc_final: 0.8630 (p0) REVERT: E 445 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7629 (t0) outliers start: 15 outliers final: 8 residues processed: 216 average time/residue: 1.3384 time to fit residues: 321.2823 Evaluate side-chains 214 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 205 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 475 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 172 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.126409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.095342 restraints weight = 49273.741| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.48 r_work: 0.2835 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17755 Z= 0.187 Angle : 0.592 5.792 24235 Z= 0.305 Chirality : 0.041 0.169 2755 Planarity : 0.005 0.065 2860 Dihedral : 12.253 107.373 3870 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.95 % Allowed : 6.82 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.18), residues: 1960 helix: 1.95 (0.17), residues: 815 sheet: -0.36 (0.22), residues: 435 loop : 0.15 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 446 TYR 0.014 0.002 TYR D 14 PHE 0.022 0.002 PHE D 99 TRP 0.011 0.002 TRP C 148 HIS 0.006 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (17715) covalent geometry : angle 0.57631 / 0.30 (24125) SS BOND : bond 0.00826 / 0.44 ( 10) SS BOND : angle 1.89927 / 1.16 ( 20) hydrogen bonds : bond 0.06146 / 3.97 ( 846) hydrogen bonds : angle 4.90360 / 3.44 ( 2748) link_BETA1-4 : bond 0.00272 / 0.15 ( 15) link_BETA1-4 : angle 1.64532 / 1.15 ( 45) link_NAG-ASN : bond 0.00174 / 0.09 ( 15) link_NAG-ASN : angle 2.51909 / 1.61 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 0.901 Fit side-chains REVERT: A 445 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8069 (t0) REVERT: B 159 MET cc_start: 0.8990 (ttp) cc_final: 0.8674 (ttp) REVERT: B 196 ASP cc_start: 0.8930 (p0) cc_final: 0.8658 (p0) REVERT: C 431 GLU cc_start: 0.7718 (pp20) cc_final: 0.7313 (pt0) REVERT: C 446 ARG cc_start: 0.8546 (tpp80) cc_final: 0.8270 (tpp80) REVERT: D 40 MET cc_start: 0.8651 (mtp) cc_final: 0.8366 (mtp) REVERT: D 210 TYR cc_start: 0.8644 (m-80) cc_final: 0.8332 (m-80) REVERT: E 196 ASP cc_start: 0.8907 (p0) cc_final: 0.8573 (p0) REVERT: E 445 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7634 (t0) outliers start: 17 outliers final: 11 residues processed: 218 average time/residue: 1.4140 time to fit residues: 343.2818 Evaluate side-chains 214 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 475 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 81 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.095533 restraints weight = 52353.489| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.52 r_work: 0.2859 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17755 Z= 0.167 Angle : 0.568 5.741 24235 Z= 0.293 Chirality : 0.040 0.163 2755 Planarity : 0.005 0.039 2860 Dihedral : 11.783 99.720 3870 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.73 % Allowed : 7.54 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.18), residues: 1960 helix: 2.04 (0.17), residues: 815 sheet: -0.36 (0.22), residues: 435 loop : 0.22 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 446 TYR 0.013 0.002 TYR D 14 PHE 0.021 0.002 PHE D 99 TRP 0.009 0.001 TRP C 148 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (17715) covalent geometry : angle 0.55252 / 0.29 (24125) SS BOND : bond 0.00827 / 0.44 ( 10) SS BOND : angle 1.81579 / 1.10 ( 20) hydrogen bonds : bond 0.05871 / 3.79 ( 846) hydrogen bonds : angle 4.82217 / 3.38 ( 2748) link_BETA1-4 : bond 0.00288 / 0.15 ( 15) link_BETA1-4 : angle 1.62190 / 1.12 ( 45) link_NAG-ASN : bond 0.00145 / 0.07 ( 15) link_NAG-ASN : angle 2.46215 / 1.58 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.920 Fit side-chains REVERT: B 159 MET cc_start: 0.8972 (ttp) cc_final: 0.8672 (ttp) REVERT: B 196 ASP cc_start: 0.8935 (p0) cc_final: 0.8656 (p0) REVERT: C 431 GLU cc_start: 0.7716 (pp20) cc_final: 0.7297 (pt0) REVERT: C 446 ARG cc_start: 0.8532 (tpp80) cc_final: 0.8255 (tpp80) REVERT: D 40 MET cc_start: 0.8624 (mtp) cc_final: 0.8333 (mtp) REVERT: D 210 TYR cc_start: 0.8687 (m-80) cc_final: 0.8379 (m-80) REVERT: E 445 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7598 (t0) outliers start: 13 outliers final: 10 residues processed: 216 average time/residue: 1.4581 time to fit residues: 350.9806 Evaluate side-chains 212 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 201 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 475 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 178 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.126135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.095350 restraints weight = 46851.374| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.44 r_work: 0.2843 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17755 Z= 0.208 Angle : 0.611 5.849 24235 Z= 0.316 Chirality : 0.042 0.174 2755 Planarity : 0.005 0.047 2860 Dihedral : 11.864 97.315 3870 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.01 % Allowed : 7.71 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.18), residues: 1960 helix: 1.94 (0.17), residues: 815 sheet: -0.36 (0.22), residues: 435 loop : 0.21 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 446 TYR 0.016 0.002 TYR A 273 PHE 0.026 0.002 PHE D 99 TRP 0.010 0.002 TRP B 148 HIS 0.007 0.002 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (17715) covalent geometry : angle 0.59563 / 0.31 (24125) SS BOND : bond 0.00837 / 0.44 ( 10) SS BOND : angle 2.03820 / 1.25 ( 20) hydrogen bonds : bond 0.06304 / 4.07 ( 846) hydrogen bonds : angle 4.93046 / 3.46 ( 2748) link_BETA1-4 : bond 0.00243 / 0.12 ( 15) link_BETA1-4 : angle 1.66803 / 1.17 ( 45) link_NAG-ASN : bond 0.00178 / 0.08 ( 15) link_NAG-ASN : angle 2.44266 / 1.55 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.912 Fit side-chains REVERT: A 445 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8095 (t0) REVERT: B 159 MET cc_start: 0.8977 (ttp) cc_final: 0.8654 (ttp) REVERT: B 196 ASP cc_start: 0.8975 (p0) cc_final: 0.8683 (p0) REVERT: C 128 TYR cc_start: 0.8765 (t80) cc_final: 0.8469 (t80) REVERT: C 431 GLU cc_start: 0.7669 (pp20) cc_final: 0.7254 (pt0) REVERT: C 446 ARG cc_start: 0.8538 (tpp80) cc_final: 0.8266 (tpp80) REVERT: D 210 TYR cc_start: 0.8686 (m-80) cc_final: 0.8340 (m-80) REVERT: E 196 ASP cc_start: 0.8887 (p0) cc_final: 0.8579 (p0) REVERT: E 445 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7626 (t0) outliers start: 18 outliers final: 11 residues processed: 210 average time/residue: 1.4351 time to fit residues: 334.8309 Evaluate side-chains 215 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 475 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 52 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.095318 restraints weight = 52004.745| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.52 r_work: 0.2843 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17755 Z= 0.176 Angle : 0.573 5.642 24235 Z= 0.297 Chirality : 0.041 0.167 2755 Planarity : 0.005 0.038 2860 Dihedral : 11.539 93.619 3870 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.78 % Allowed : 8.21 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.18), residues: 1960 helix: 1.99 (0.17), residues: 815 sheet: -0.38 (0.22), residues: 435 loop : 0.22 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 446 TYR 0.013 0.002 TYR D 14 PHE 0.021 0.002 PHE D 99 TRP 0.009 0.002 TRP A 133 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (17715) covalent geometry : angle 0.55833 / 0.29 (24125) SS BOND : bond 0.00823 / 0.44 ( 10) SS BOND : angle 1.82838 / 1.12 ( 20) hydrogen bonds : bond 0.05982 / 3.86 ( 846) hydrogen bonds : angle 4.85269 / 3.40 ( 2748) link_BETA1-4 : bond 0.00308 / 0.16 ( 15) link_BETA1-4 : angle 1.60481 / 1.11 ( 45) link_NAG-ASN : bond 0.00157 / 0.08 ( 15) link_NAG-ASN : angle 2.43679 / 1.57 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 0.898 Fit side-chains REVERT: A 445 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8073 (t0) REVERT: B 159 MET cc_start: 0.8973 (ttp) cc_final: 0.8673 (ttp) REVERT: B 196 ASP cc_start: 0.8991 (p0) cc_final: 0.8715 (p0) REVERT: C 431 GLU cc_start: 0.7668 (pp20) cc_final: 0.7245 (pt0) REVERT: C 446 ARG cc_start: 0.8547 (tpp80) cc_final: 0.8271 (tpp80) REVERT: D 210 TYR cc_start: 0.8691 (m-80) cc_final: 0.8325 (m-80) REVERT: D 446 ARG cc_start: 0.8583 (tpp80) cc_final: 0.8267 (tpp80) REVERT: E 196 ASP cc_start: 0.8903 (p0) cc_final: 0.8576 (p0) REVERT: E 445 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7619 (t0) outliers start: 14 outliers final: 11 residues processed: 213 average time/residue: 1.4250 time to fit residues: 337.2877 Evaluate side-chains 216 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 475 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 81 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 0.0370 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.127097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.095707 restraints weight = 53287.723| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.53 r_work: 0.2837 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17755 Z= 0.156 Angle : 0.555 5.618 24235 Z= 0.287 Chirality : 0.040 0.159 2755 Planarity : 0.004 0.039 2860 Dihedral : 11.177 92.073 3870 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.73 % Allowed : 8.44 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.18), residues: 1960 helix: 2.07 (0.17), residues: 815 sheet: -0.37 (0.22), residues: 435 loop : 0.26 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 98 TYR 0.012 0.002 TYR D 14 PHE 0.020 0.002 PHE D 99 TRP 0.009 0.001 TRP A 133 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (17715) covalent geometry : angle 0.54013 / 0.28 (24125) SS BOND : bond 0.00818 / 0.44 ( 10) SS BOND : angle 1.74777 / 1.07 ( 20) hydrogen bonds : bond 0.05736 / 3.70 ( 846) hydrogen bonds : angle 4.78190 / 3.35 ( 2748) link_BETA1-4 : bond 0.00282 / 0.15 ( 15) link_BETA1-4 : angle 1.56392 / 1.08 ( 45) link_NAG-ASN : bond 0.00136 / 0.06 ( 15) link_NAG-ASN : angle 2.42934 / 1.56 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.931 Fit side-chains REVERT: A 445 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8085 (t0) REVERT: B 159 MET cc_start: 0.8968 (ttp) cc_final: 0.8683 (ttp) REVERT: B 196 ASP cc_start: 0.8992 (p0) cc_final: 0.8706 (p0) REVERT: C 431 GLU cc_start: 0.7712 (pp20) cc_final: 0.7293 (pt0) REVERT: C 446 ARG cc_start: 0.8548 (tpp80) cc_final: 0.8284 (tpp80) REVERT: D 210 TYR cc_start: 0.8691 (m-80) cc_final: 0.8395 (m-80) REVERT: D 446 ARG cc_start: 0.8583 (tpp80) cc_final: 0.8275 (tpp80) REVERT: E 445 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7604 (t0) outliers start: 13 outliers final: 11 residues processed: 207 average time/residue: 1.4341 time to fit residues: 331.7222 Evaluate side-chains 214 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 475 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.0070 chunk 49 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.127295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.096027 restraints weight = 52357.058| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.52 r_work: 0.2843 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17755 Z= 0.153 Angle : 0.552 5.627 24235 Z= 0.285 Chirality : 0.040 0.159 2755 Planarity : 0.004 0.038 2860 Dihedral : 11.007 91.111 3870 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.73 % Allowed : 8.55 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.18), residues: 1960 helix: 2.11 (0.17), residues: 815 sheet: -0.37 (0.22), residues: 435 loop : 0.29 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 446 TYR 0.013 0.002 TYR A 273 PHE 0.031 0.002 PHE C 99 TRP 0.009 0.001 TRP A 133 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (17715) covalent geometry : angle 0.53717 / 0.28 (24125) SS BOND : bond 0.00819 / 0.44 ( 10) SS BOND : angle 1.72656 / 1.05 ( 20) hydrogen bonds : bond 0.05674 / 3.66 ( 846) hydrogen bonds : angle 4.75830 / 3.33 ( 2748) link_BETA1-4 : bond 0.00291 / 0.15 ( 15) link_BETA1-4 : angle 1.54923 / 1.07 ( 45) link_NAG-ASN : bond 0.00132 / 0.06 ( 15) link_NAG-ASN : angle 2.41936 / 1.56 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 0.894 Fit side-chains REVERT: A 445 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8074 (t0) REVERT: B 159 MET cc_start: 0.8956 (ttp) cc_final: 0.8666 (ttp) REVERT: B 196 ASP cc_start: 0.8983 (p0) cc_final: 0.8700 (p0) REVERT: C 431 GLU cc_start: 0.7710 (pp20) cc_final: 0.7292 (pt0) REVERT: C 446 ARG cc_start: 0.8533 (tpp80) cc_final: 0.8277 (tpp80) REVERT: D 210 TYR cc_start: 0.8692 (m-80) cc_final: 0.8396 (m-80) REVERT: D 446 ARG cc_start: 0.8563 (tpp80) cc_final: 0.8247 (tpp80) REVERT: E 445 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7584 (t0) outliers start: 13 outliers final: 10 residues processed: 206 average time/residue: 1.4575 time to fit residues: 332.8653 Evaluate side-chains 214 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 178 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.096673 restraints weight = 53906.328| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.54 r_work: 0.2860 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17755 Z= 0.135 Angle : 0.527 5.451 24235 Z= 0.272 Chirality : 0.039 0.151 2755 Planarity : 0.004 0.039 2860 Dihedral : 10.657 90.781 3870 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.67 % Allowed : 8.55 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.18), residues: 1960 helix: 2.24 (0.17), residues: 815 sheet: -0.34 (0.22), residues: 435 loop : 0.33 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 446 TYR 0.011 0.001 TYR E 210 PHE 0.021 0.001 PHE C 99 TRP 0.008 0.001 TRP A 133 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (17715) covalent geometry : angle 0.51223 / 0.27 (24125) SS BOND : bond 0.00813 / 0.44 ( 10) SS BOND : angle 1.61693 / 0.99 ( 20) hydrogen bonds : bond 0.05368 / 3.46 ( 846) hydrogen bonds : angle 4.65129 / 3.25 ( 2748) link_BETA1-4 : bond 0.00304 / 0.16 ( 15) link_BETA1-4 : angle 1.49816 / 1.03 ( 45) link_NAG-ASN : bond 0.00128 / 0.06 ( 15) link_NAG-ASN : angle 2.37168 / 1.53 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12697.47 seconds wall clock time: 215 minutes 23.04 seconds (12923.04 seconds total)