Starting phenix.real_space_refine on Wed May 6 00:50:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v88_43030/05_2026/8v88_43030_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v88_43030/05_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_43030/05_2026/8v88_43030_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v88_43030/05_2026/8v88_43030_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v88_43030/05_2026/8v88_43030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v88_43030/05_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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, 231 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 3, 'YLI': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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, 184 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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, 184 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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, 184 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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, 137 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 1, 'YLI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 10.42, per 1000 atoms: 0.31 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: 2.90 Conformation dependent library (CDL) restraints added in 1.4 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: 0.88 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: 7.76 Time building geometry restraints manager: 4.11 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 0.340 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 36.020 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 covalent geometry : bond 0.00625 (17715) covalent geometry : angle 0.82083 (24125) SS BOND : bond 0.00764 ( 10) SS BOND : angle 1.72415 ( 20) hydrogen bonds : bond 0.19838 ( 846) hydrogen bonds : angle 6.95813 ( 2748) link_BETA1-4 : bond 0.00328 ( 15) link_BETA1-4 : angle 1.83529 ( 45) link_NAG-ASN : bond 0.00253 ( 15) link_NAG-ASN : angle 2.71576 ( 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 : 0.954 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: 1.6730 time to fit residues: 422.3357 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 : 0.913 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3457 r_free = 0.3457 target = 0.129869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.098013 restraints weight = 55464.745| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.59 r_work: 0.2885 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 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 = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17755 Z= 0.136 Angle : 0.588 5.555 24235 Z= 0.296 Chirality : 0.041 0.148 2755 Planarity : 0.004 0.039 2860 Dihedral : 16.110 149.748 3870 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.73 % Allowed : 5.36 % Favored : 93.91 % 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: 0.81 (0.18), residues: 1960 helix: 1.54 (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 E 446 TYR 0.009 0.001 TYR C 210 PHE 0.011 0.001 PHE A 99 TRP 0.007 0.001 TRP B 307 HIS 0.002 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00275 (17715) covalent geometry : angle 0.57287 (24125) SS BOND : bond 0.00816 ( 10) SS BOND : angle 1.61271 ( 20) hydrogen bonds : bond 0.06170 ( 846) hydrogen bonds : angle 5.04911 ( 2748) link_BETA1-4 : bond 0.00291 ( 15) link_BETA1-4 : angle 1.89154 ( 45) link_NAG-ASN : bond 0.00152 ( 15) link_NAG-ASN : angle 2.34709 ( 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 226 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 213 time to evaluate : 0.937 Fit side-chains REVERT: B 159 MET cc_start: 0.8950 (ttp) cc_final: 0.8727 (ttp) REVERT: B 163 ASP cc_start: 0.8827 (t70) cc_final: 0.8555 (t70) REVERT: B 196 ASP cc_start: 0.8898 (p0) cc_final: 0.8626 (p0) REVERT: B 446 ARG cc_start: 0.8645 (tpp80) cc_final: 0.8422 (tpp80) REVERT: C 170 ASN cc_start: 0.7736 (t0) cc_final: 0.7525 (t0) REVERT: C 210 TYR cc_start: 0.8636 (m-80) cc_final: 0.8284 (m-80) REVERT: C 431 GLU cc_start: 0.7784 (pp20) cc_final: 0.7399 (pt0) REVERT: D 163 ASP cc_start: 0.8838 (t70) cc_final: 0.8582 (t70) REVERT: D 260 MET cc_start: 0.8630 (mmp) cc_final: 0.8376 (mmp) REVERT: E 170 ASN cc_start: 0.7647 (t0) cc_final: 0.7410 (t0) outliers start: 13 outliers final: 7 residues processed: 217 average time/residue: 1.6458 time to fit residues: 392.2014 Evaluate side-chains 210 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 203 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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: 0.8980 chunk 16 optimal weight: 0.0770 chunk 112 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3443 r_free = 0.3443 target = 0.128401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.097242 restraints weight = 50994.493| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.51 r_work: 0.2881 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- 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 = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1650 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= 0.136 Angle : 0.560 7.536 24235 Z= 0.281 Chirality : 0.040 0.151 2755 Planarity : 0.004 0.036 2860 Dihedral : 13.737 124.387 3870 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.67 % Allowed : 6.15 % Favored : 93.18 % 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: 1.21 (0.18), residues: 1960 helix: 2.02 (0.17), residues: 815 sheet: -0.23 (0.22), residues: 445 loop : 0.18 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 185 TYR 0.017 0.002 TYR E 14 PHE 0.014 0.001 PHE D 99 TRP 0.008 0.001 TRP B 148 HIS 0.004 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00288 (17715) covalent geometry : angle 0.54397 (24125) SS BOND : bond 0.00809 ( 10) SS BOND : angle 1.56494 ( 20) hydrogen bonds : bond 0.05841 ( 846) hydrogen bonds : angle 4.77735 ( 2748) link_BETA1-4 : bond 0.00353 ( 15) link_BETA1-4 : angle 1.68912 ( 45) link_NAG-ASN : bond 0.00119 ( 15) link_NAG-ASN : angle 2.46322 ( 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 228 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 216 time to evaluate : 0.900 Fit side-chains REVERT: A 247 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7461 (tp) REVERT: B 159 MET cc_start: 0.8967 (ttp) cc_final: 0.8695 (ttp) REVERT: B 196 ASP cc_start: 0.8918 (p0) cc_final: 0.8636 (p0) REVERT: C 26 GLN cc_start: 0.8721 (mm110) cc_final: 0.8520 (mm110) REVERT: C 128 TYR cc_start: 0.8757 (t80) cc_final: 0.8468 (t80) REVERT: C 170 ASN cc_start: 0.7909 (t0) cc_final: 0.7697 (t0) REVERT: C 191 LYS cc_start: 0.8365 (mmtt) cc_final: 0.8134 (mmtt) REVERT: C 431 GLU cc_start: 0.7696 (pp20) cc_final: 0.7289 (pt0) REVERT: C 446 ARG cc_start: 0.8511 (tpp80) cc_final: 0.8256 (tpp80) REVERT: D 40 MET cc_start: 0.8605 (mtp) cc_final: 0.8307 (mtp) REVERT: D 57 MET cc_start: 0.9251 (mtm) cc_final: 0.9035 (mtp) REVERT: D 210 TYR cc_start: 0.8660 (m-80) cc_final: 0.8335 (m-80) REVERT: E 445 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7529 (t0) outliers start: 12 outliers final: 4 residues processed: 219 average time/residue: 1.6180 time to fit residues: 389.1301 Evaluate side-chains 210 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 204 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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: 2.9990 chunk 187 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 121 optimal weight: 0.0020 chunk 170 optimal weight: 2.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.126832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.095522 restraints weight = 51189.262| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.52 r_work: 0.2850 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 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 = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1794 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= 0.179 Angle : 0.593 7.168 24235 Z= 0.302 Chirality : 0.041 0.165 2755 Planarity : 0.005 0.068 2860 Dihedral : 12.607 111.281 3870 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.84 % Allowed : 6.42 % Favored : 92.74 % 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: 2.03 (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 0.007 0.001 ARG D 446 TYR 0.015 0.002 TYR B 14 PHE 0.022 0.002 PHE D 99 TRP 0.010 0.002 TRP C 148 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00397 (17715) covalent geometry : angle 0.57738 (24125) SS BOND : bond 0.00811 ( 10) SS BOND : angle 1.87726 ( 20) hydrogen bonds : bond 0.06035 ( 846) hydrogen bonds : angle 4.86412 ( 2748) link_BETA1-4 : bond 0.00266 ( 15) link_BETA1-4 : angle 1.66500 ( 45) link_NAG-ASN : bond 0.00169 ( 15) link_NAG-ASN : angle 2.57326 ( 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 228 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.8984 (ttp) cc_final: 0.8666 (ttp) REVERT: B 196 ASP cc_start: 0.8950 (p0) cc_final: 0.8670 (p0) REVERT: C 57 MET cc_start: 0.9324 (mtm) cc_final: 0.9089 (mtp) REVERT: C 431 GLU cc_start: 0.7715 (pp20) cc_final: 0.7316 (pt0) REVERT: C 446 ARG cc_start: 0.8539 (tpp80) cc_final: 0.8279 (tpp80) REVERT: D 40 MET cc_start: 0.8634 (mtp) cc_final: 0.8328 (mtp) REVERT: D 210 TYR cc_start: 0.8635 (m-80) cc_final: 0.8316 (m-80) REVERT: E 196 ASP cc_start: 0.8913 (p0) cc_final: 0.8584 (p0) REVERT: E 445 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7608 (t0) outliers start: 15 outliers final: 10 residues processed: 219 average time/residue: 1.6777 time to fit residues: 405.5646 Evaluate side-chains 213 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 161 GLU Chi-restraints excluded: chain D residue 445 ASP 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: 3.9990 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3422 r_free = 0.3422 target = 0.126715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.095708 restraints weight = 49179.519| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.49 r_work: 0.2858 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 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 = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1883 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= 0.175 Angle : 0.577 5.794 24235 Z= 0.297 Chirality : 0.041 0.165 2755 Planarity : 0.005 0.037 2860 Dihedral : 12.000 105.188 3870 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.84 % Allowed : 6.98 % Favored : 92.18 % 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: 2.01 (0.17), residues: 815 sheet: -0.35 (0.22), residues: 435 loop : 0.16 (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 0.010 0.002 TRP C 148 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00386 (17715) covalent geometry : angle 0.56121 (24125) SS BOND : bond 0.00817 ( 10) SS BOND : angle 1.85612 ( 20) hydrogen bonds : bond 0.06012 ( 846) hydrogen bonds : angle 4.85806 ( 2748) link_BETA1-4 : bond 0.00294 ( 15) link_BETA1-4 : angle 1.59955 ( 45) link_NAG-ASN : bond 0.00167 ( 15) link_NAG-ASN : angle 2.55504 ( 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 224 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.884 Fit side-chains REVERT: A 445 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7940 (t0) REVERT: B 159 MET cc_start: 0.8979 (ttp) cc_final: 0.8676 (ttp) REVERT: B 196 ASP cc_start: 0.8927 (p0) cc_final: 0.8644 (p0) REVERT: C 57 MET cc_start: 0.9316 (mtm) cc_final: 0.9111 (mtp) REVERT: C 431 GLU cc_start: 0.7703 (pp20) cc_final: 0.7303 (pt0) REVERT: C 446 ARG cc_start: 0.8539 (tpp80) cc_final: 0.8263 (tpp80) REVERT: D 40 MET cc_start: 0.8626 (mtp) cc_final: 0.8353 (mtp) REVERT: D 210 TYR cc_start: 0.8619 (m-80) cc_final: 0.8233 (m-80) REVERT: E 196 ASP cc_start: 0.8896 (p0) cc_final: 0.8567 (p0) REVERT: E 445 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7592 (t0) outliers start: 15 outliers final: 11 residues processed: 215 average time/residue: 1.6447 time to fit residues: 388.6146 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 : 0.915 ------------------------------------------------------------------------------- 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: 2.9990 chunk 60 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3415 r_free = 0.3415 target = 0.126139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.094701 restraints weight = 52044.320| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.52 r_work: 0.2831 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17755 Z= 0.208 Angle : 0.613 5.924 24235 Z= 0.317 Chirality : 0.042 0.173 2755 Planarity : 0.005 0.064 2860 Dihedral : 11.985 99.288 3870 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.12 % Allowed : 7.32 % Favored : 91.56 % 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: 1.94 (0.17), residues: 815 sheet: -0.36 (0.22), residues: 435 loop : 0.19 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 446 TYR 0.016 0.002 TYR D 14 PHE 0.026 0.002 PHE D 99 TRP 0.010 0.002 TRP C 148 HIS 0.012 0.002 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00467 (17715) covalent geometry : angle 0.59740 (24125) SS BOND : bond 0.00839 ( 10) SS BOND : angle 2.04811 ( 20) hydrogen bonds : bond 0.06306 ( 846) hydrogen bonds : angle 4.94001 ( 2748) link_BETA1-4 : bond 0.00250 ( 15) link_BETA1-4 : angle 1.70692 ( 45) link_NAG-ASN : bond 0.00192 ( 15) link_NAG-ASN : angle 2.47528 ( 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 227 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.985 Fit side-chains REVERT: A 445 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8096 (t0) REVERT: B 159 MET cc_start: 0.8997 (ttp) cc_final: 0.8672 (ttp) REVERT: B 196 ASP cc_start: 0.8994 (p0) cc_final: 0.8708 (p0) REVERT: C 128 TYR cc_start: 0.8784 (t80) cc_final: 0.8496 (t80) REVERT: C 431 GLU cc_start: 0.7694 (pp20) cc_final: 0.7291 (pt0) REVERT: C 446 ARG cc_start: 0.8543 (tpp80) cc_final: 0.8255 (tpp80) REVERT: D 210 TYR cc_start: 0.8627 (m-80) cc_final: 0.8313 (m-80) REVERT: E 196 ASP cc_start: 0.8907 (p0) cc_final: 0.8603 (p0) REVERT: E 445 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7647 (t0) outliers start: 20 outliers final: 11 residues processed: 214 average time/residue: 1.7105 time to fit residues: 402.7095 Evaluate side-chains 218 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 205 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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=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: 2.9990 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3416 r_free = 0.3416 target = 0.126198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.095481 restraints weight = 47016.681| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.45 r_work: 0.2859 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 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 = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1994 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= 0.203 Angle : 0.601 5.651 24235 Z= 0.312 Chirality : 0.042 0.172 2755 Planarity : 0.005 0.049 2860 Dihedral : 11.856 97.435 3870 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.78 % Allowed : 7.99 % Favored : 91.23 % 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: 1.09 (0.18), residues: 1960 helix: 1.92 (0.17), residues: 815 sheet: -0.36 (0.22), residues: 435 loop : 0.18 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 446 TYR 0.017 0.002 TYR A 273 PHE 0.024 0.002 PHE D 99 TRP 0.010 0.002 TRP A 133 HIS 0.012 0.002 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00456 (17715) covalent geometry : angle 0.58563 (24125) SS BOND : bond 0.00826 ( 10) SS BOND : angle 2.01267 ( 20) hydrogen bonds : bond 0.06268 ( 846) hydrogen bonds : angle 4.92834 ( 2748) link_BETA1-4 : bond 0.00284 ( 15) link_BETA1-4 : angle 1.63962 ( 45) link_NAG-ASN : bond 0.00180 ( 15) link_NAG-ASN : angle 2.44005 ( 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 221 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 0.918 Fit side-chains REVERT: A 445 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8098 (t0) REVERT: B 159 MET cc_start: 0.8970 (ttp) cc_final: 0.8672 (ttp) REVERT: B 196 ASP cc_start: 0.8972 (p0) cc_final: 0.8683 (p0) REVERT: C 446 ARG cc_start: 0.8545 (tpp80) cc_final: 0.8267 (tpp80) REVERT: D 210 TYR cc_start: 0.8634 (m-80) cc_final: 0.8251 (m-80) REVERT: E 196 ASP cc_start: 0.8886 (p0) cc_final: 0.8581 (p0) REVERT: E 445 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7634 (t0) outliers start: 14 outliers final: 11 residues processed: 213 average time/residue: 1.6719 time to fit residues: 392.3693 Evaluate side-chains 218 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 205 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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: 0.7980 chunk 100 optimal weight: 3.9990 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: 0.9990 chunk 35 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.127451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.096287 restraints weight = 52067.721| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.52 r_work: 0.2848 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- 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 = 0.36 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 | |-----------------------------------------------------------------------------| r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2090 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= 0.143 Angle : 0.540 5.512 24235 Z= 0.279 Chirality : 0.040 0.154 2755 Planarity : 0.004 0.045 2860 Dihedral : 11.204 93.285 3870 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.61 % Allowed : 8.49 % Favored : 90.89 % 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: 1.25 (0.18), residues: 1960 helix: 2.10 (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 0.000 ARG D 446 TYR 0.010 0.002 TYR D 14 PHE 0.017 0.001 PHE D 99 TRP 0.009 0.001 TRP A 133 HIS 0.007 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00311 (17715) covalent geometry : angle 0.52482 (24125) SS BOND : bond 0.00809 ( 10) SS BOND : angle 1.64504 ( 20) hydrogen bonds : bond 0.05571 ( 846) hydrogen bonds : angle 4.74285 ( 2748) link_BETA1-4 : bond 0.00297 ( 15) link_BETA1-4 : angle 1.56224 ( 45) link_NAG-ASN : bond 0.00139 ( 15) link_NAG-ASN : angle 2.41262 ( 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: 11 poor density : 209 time to evaluate : 0.896 Fit side-chains REVERT: B 159 MET cc_start: 0.8950 (ttp) cc_final: 0.8662 (ttp) REVERT: B 196 ASP cc_start: 0.8923 (p0) cc_final: 0.8633 (p0) REVERT: C 431 GLU cc_start: 0.7692 (pp20) cc_final: 0.7276 (pt0) REVERT: C 446 ARG cc_start: 0.8548 (tpp80) cc_final: 0.8278 (tpp80) REVERT: D 210 TYR cc_start: 0.8652 (m-80) cc_final: 0.8331 (m-80) REVERT: E 445 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7574 (t0) outliers start: 11 outliers final: 7 residues processed: 211 average time/residue: 1.6119 time to fit residues: 373.5535 Evaluate side-chains 211 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 255 LEU Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 81 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 165 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3456 r_free = 0.3456 target = 0.129240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.098258 restraints weight = 53128.622| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.53 r_work: 0.2902 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17755 Z= 0.111 Angle : 0.499 5.149 24235 Z= 0.256 Chirality : 0.039 0.138 2755 Planarity : 0.004 0.042 2860 Dihedral : 10.392 91.391 3870 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.39 % Allowed : 8.94 % Favored : 90.67 % 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: 1.51 (0.18), residues: 1960 helix: 2.33 (0.17), residues: 815 sheet: -0.24 (0.22), residues: 445 loop : 0.39 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 446 TYR 0.009 0.001 TYR A 210 PHE 0.010 0.001 PHE D 99 TRP 0.008 0.001 TRP A 133 HIS 0.004 0.000 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00236 (17715) covalent geometry : angle 0.48478 (24125) SS BOND : bond 0.00809 ( 10) SS BOND : angle 1.43924 ( 20) hydrogen bonds : bond 0.04967 ( 846) hydrogen bonds : angle 4.51368 ( 2748) link_BETA1-4 : bond 0.00336 ( 15) link_BETA1-4 : angle 1.45033 ( 45) link_NAG-ASN : bond 0.00138 ( 15) link_NAG-ASN : angle 2.30957 ( 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 222 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 215 time to evaluate : 0.909 Fit side-chains REVERT: B 196 ASP cc_start: 0.8902 (p0) cc_final: 0.8656 (p0) REVERT: C 38 GLN cc_start: 0.8848 (tt0) cc_final: 0.8601 (tt0) REVERT: C 431 GLU cc_start: 0.7707 (pp20) cc_final: 0.7290 (pt0) REVERT: C 446 ARG cc_start: 0.8500 (tpp80) cc_final: 0.8276 (tpp80) REVERT: D 210 TYR cc_start: 0.8627 (m-80) cc_final: 0.8297 (m-80) REVERT: D 446 ARG cc_start: 0.8550 (tpp80) cc_final: 0.8266 (tpp80) outliers start: 7 outliers final: 5 residues processed: 217 average time/residue: 1.6412 time to fit residues: 393.5107 Evaluate side-chains 211 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 206 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 247 LEU 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: 0.9980 chunk 49 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3443 r_free = 0.3443 target = 0.128210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.097124 restraints weight = 52209.048| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.52 r_work: 0.2858 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- 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 = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2205 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 : 0.524 5.369 24235 Z= 0.269 Chirality : 0.039 0.151 2755 Planarity : 0.004 0.044 2860 Dihedral : 10.448 90.682 3870 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.34 % Allowed : 8.94 % 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: 1.52 (0.18), residues: 1960 helix: 2.38 (0.17), residues: 815 sheet: -0.30 (0.22), residues: 435 loop : 0.37 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 446 TYR 0.012 0.001 TYR E 210 PHE 0.017 0.001 PHE C 99 TRP 0.007 0.001 TRP C 148 HIS 0.005 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00295 (17715) covalent geometry : angle 0.50940 (24125) SS BOND : bond 0.00808 ( 10) SS BOND : angle 1.62463 ( 20) hydrogen bonds : bond 0.05264 ( 846) hydrogen bonds : angle 4.58404 ( 2748) link_BETA1-4 : bond 0.00303 ( 15) link_BETA1-4 : angle 1.44932 ( 45) link_NAG-ASN : bond 0.00125 ( 15) link_NAG-ASN : angle 2.32032 ( 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 213 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 207 time to evaluate : 0.809 Fit side-chains REVERT: B 196 ASP cc_start: 0.8975 (p0) cc_final: 0.8707 (p0) REVERT: C 38 GLN cc_start: 0.8897 (tt0) cc_final: 0.8651 (tt0) REVERT: C 128 TYR cc_start: 0.8701 (t80) cc_final: 0.8370 (t80) REVERT: C 431 GLU cc_start: 0.7712 (pp20) cc_final: 0.7308 (pt0) REVERT: C 446 ARG cc_start: 0.8497 (tpp80) cc_final: 0.8264 (tpp80) REVERT: D 210 TYR cc_start: 0.8645 (m-80) cc_final: 0.8318 (m-80) REVERT: D 446 ARG cc_start: 0.8535 (tpp80) cc_final: 0.8240 (tpp80) outliers start: 6 outliers final: 5 residues processed: 208 average time/residue: 1.5976 time to fit residues: 364.7440 Evaluate side-chains 207 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 202 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 178 optimal weight: 0.0470 chunk 159 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.098887 restraints weight = 53671.930| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.53 r_work: 0.2884 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17755 Z= 0.107 Angle : 0.492 5.508 24235 Z= 0.251 Chirality : 0.038 0.136 2755 Planarity : 0.004 0.040 2860 Dihedral : 10.027 90.623 3870 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.22 % Allowed : 9.22 % Favored : 90.56 % 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: 1.68 (0.18), residues: 1960 helix: 2.50 (0.17), residues: 815 sheet: -0.19 (0.22), residues: 445 loop : 0.46 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 446 TYR 0.008 0.001 TYR A 210 PHE 0.010 0.001 PHE D 99 TRP 0.007 0.001 TRP A 133 HIS 0.004 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00226 (17715) covalent geometry : angle 0.47722 (24125) SS BOND : bond 0.00795 ( 10) SS BOND : angle 1.40796 ( 20) hydrogen bonds : bond 0.04774 ( 846) hydrogen bonds : angle 4.42284 ( 2748) link_BETA1-4 : bond 0.00326 ( 15) link_BETA1-4 : angle 1.42039 ( 45) link_NAG-ASN : bond 0.00126 ( 15) link_NAG-ASN : angle 2.27184 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13807.65 seconds wall clock time: 233 minutes 43.45 seconds (14023.45 seconds total)