Starting phenix.real_space_refine on Tue May 5 22:24:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nx1_49898/05_2026/9nx1_49898_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nx1_49898/05_2026/9nx1_49898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nx1_49898/05_2026/9nx1_49898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nx1_49898/05_2026/9nx1_49898.map" model { file = "/net/cci-nas-00/data/ceres_data/9nx1_49898/05_2026/9nx1_49898_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nx1_49898/05_2026/9nx1_49898_trim.cif" } resolution = 3.1 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= 0.002 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 114 5.16 5 Cl 5 4.86 5 C 10567 2.51 5 N 2590 2.21 5 O 2941 1.98 5 H 15734 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 31951 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 196 Classifications: {'peptide': 12} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 11} Chain: "B" Number of atoms: 6281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 6281 Classifications: {'peptide': 391} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "C" Number of atoms: 6281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 6281 Classifications: {'peptide': 391} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "D" Number of atoms: 6281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 6281 Classifications: {'peptide': 391} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "E" Number of atoms: 6281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 6281 Classifications: {'peptide': 391} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "F" Number of atoms: 6281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 6281 Classifications: {'peptide': 391} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.84, per 1000 atoms: 0.18 Number of scatterers: 31951 At special positions: 0 Unit cell: (93.003, 91.934, 165.695, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 5 17.00 S 114 16.00 O 2941 8.00 N 2590 7.00 C 10567 6.00 H 15734 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 2 " - pdb=" SG CYS A 8 " distance=2.03 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 12 " distance=2.03 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 Simple disulfide: pdb=" SG CYS F 127 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 189 " - pdb=" SG CYS F 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG B 501 " - " ASN B 23 " " NAG B 502 " - " ASN B 67 " " NAG C 501 " - " ASN C 23 " " NAG C 502 " - " ASN C 67 " " NAG D 501 " - " ASN D 23 " " NAG D 502 " - " ASN D 67 " " NAG E 501 " - " ASN E 23 " " NAG E 502 " - " ASN E 67 " " NAG F 501 " - " ASN F 23 " " NAG F 502 " - " ASN F 67 " " NAG G 1 " - " ASN B 110 " " NAG H 1 " - " ASN C 110 " " NAG I 1 " - " ASN D 110 " " NAG J 1 " - " ASN E 110 " " NAG K 1 " - " ASN F 110 " Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 901.9 milliseconds 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3754 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 20 sheets defined 44.7% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.622A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.592A pdb=" N GLN B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE B 84 " --> pdb=" O ASP B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 84' Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 214 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 235 through 238 removed outlier: 3.788A pdb=" N LYS B 238 " --> pdb=" O SER B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 235 through 238' Processing helix chain 'B' and resid 239 through 259 removed outlier: 3.540A pdb=" N ILE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 296 Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.563A pdb=" N ARG B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 466 Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.596A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.593A pdb=" N GLN C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE C 84 " --> pdb=" O ASP C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 84' Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 214 through 228 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 239 through 260 removed outlier: 3.675A pdb=" N ILE C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 296 Processing helix chain 'C' and resid 306 through 320 Processing helix chain 'C' and resid 409 through 466 Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.574A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.600A pdb=" N GLN D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE D 84 " --> pdb=" O ASP D 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 80 through 84' Processing helix chain 'D' and resid 207 through 214 Processing helix chain 'D' and resid 214 through 228 Processing helix chain 'D' and resid 229 through 231 No H-bonds generated for 'chain 'D' and resid 229 through 231' Processing helix chain 'D' and resid 239 through 259 Processing helix chain 'D' and resid 268 through 296 Processing helix chain 'D' and resid 305 through 320 removed outlier: 3.577A pdb=" N ARG D 309 " --> pdb=" O PRO D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 466 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.584A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.564A pdb=" N GLN E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE E 84 " --> pdb=" O ASP E 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 80 through 84' Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'E' and resid 214 through 227 Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 239 through 259 removed outlier: 3.590A pdb=" N ILE E 259 " --> pdb=" O LEU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 296 Processing helix chain 'E' and resid 306 through 320 Processing helix chain 'E' and resid 409 through 466 Processing helix chain 'E' and resid 469 through 478 Processing helix chain 'F' and resid 2 through 11 removed outlier: 3.558A pdb=" N VAL F 11 " --> pdb=" O TYR F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.632A pdb=" N GLN F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE F 84 " --> pdb=" O ASP F 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 80 through 84' Processing helix chain 'F' and resid 207 through 214 Processing helix chain 'F' and resid 214 through 228 Processing helix chain 'F' and resid 229 through 231 No H-bonds generated for 'chain 'F' and resid 229 through 231' Processing helix chain 'F' and resid 237 through 259 removed outlier: 3.508A pdb=" N LEU F 241 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 296 Processing helix chain 'F' and resid 305 through 320 removed outlier: 3.557A pdb=" N ARG F 309 " --> pdb=" O PRO F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 466 Processing helix chain 'F' and resid 469 through 478 Processing sheet with id=AA1, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.084A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.084A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL B 48 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASP B 41 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR B 60 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N THR B 29 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.539A pdb=" N GLY B 146 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.539A pdb=" N GLY B 146 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 185 " --> pdb=" O TYR B 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.514A pdb=" N ASN C 110 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.514A pdb=" N ASN C 110 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C 48 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL C 42 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR C 50 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP C 54 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU C 36 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN C 56 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU C 34 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N SER C 58 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N PHE C 32 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N THR C 60 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N VAL C 30 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.532A pdb=" N LEU C 90 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 146 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.532A pdb=" N LEU C 90 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 146 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C 185 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.056A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.056A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL D 48 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL D 42 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR D 50 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP D 54 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU D 36 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN D 56 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU D 34 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N SER D 58 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N PHE D 32 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N THR D 60 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N VAL D 30 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.545A pdb=" N LEU D 90 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY D 146 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.545A pdb=" N LEU D 90 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY D 146 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 185 " --> pdb=" O TYR D 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.078A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE E 53 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.078A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL E 48 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL E 42 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR E 50 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP E 54 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU E 36 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN E 56 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU E 34 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N SER E 58 " --> pdb=" O PHE E 32 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N PHE E 32 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N THR E 60 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N VAL E 30 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.638A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.638A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG E 185 " --> pdb=" O TYR E 194 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 76 through 79 removed outlier: 3.544A pdb=" N ASN F 110 " --> pdb=" O HIS F 114 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N HIS F 114 " --> pdb=" O ASN F 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 76 through 79 removed outlier: 3.544A pdb=" N ASN F 110 " --> pdb=" O HIS F 114 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N HIS F 114 " --> pdb=" O ASN F 110 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL F 48 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL F 42 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR F 50 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP F 54 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU F 36 " --> pdb=" O TRP F 54 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN F 56 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LEU F 34 " --> pdb=" O GLN F 56 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N SER F 58 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N PHE F 32 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N THR F 60 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N VAL F 30 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU F 28 " --> pdb=" O ASP F 156 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLN F 158 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL F 30 " --> pdb=" O GLN F 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 89 through 91 removed outlier: 3.630A pdb=" N LEU F 90 " --> pdb=" O GLY F 146 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY F 146 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER F 147 " --> pdb=" O PRO F 195 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR F 202 " --> pdb=" O VAL F 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 89 through 91 removed outlier: 3.630A pdb=" N LEU F 90 " --> pdb=" O GLY F 146 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY F 146 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER F 147 " --> pdb=" O PRO F 195 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG F 185 " --> pdb=" O TYR F 194 " (cutoff:3.500A) 941 hydrogen bonds defined for protein. 2775 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: 7.57 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15694 1.04 - 1.24: 1578 1.24 - 1.44: 5730 1.44 - 1.63: 9231 1.63 - 1.83: 169 Bond restraints: 32402 Sorted by residual: bond pdb=" N GLU E 1 " pdb=" H2 GLU E 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N ALA A 1 " pdb=" H2 ALA A 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N GLU B 1 " pdb=" H3 GLU B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N GLU B 1 " pdb=" H2 GLU B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N GLU C 1 " pdb=" H3 GLU C 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 32397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.07: 58372 7.07 - 14.14: 18 14.14 - 21.22: 1 21.22 - 28.29: 39 28.29 - 35.36: 26 Bond angle restraints: 58456 Sorted by residual: angle pdb=" H1 ALA A 1 " pdb=" N ALA A 1 " pdb=" H3 ALA A 1 " ideal model delta sigma weight residual 109.47 74.11 35.36 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CE LYS F 5 " pdb=" CD LYS F 5 " pdb=" HD2 LYS F 5 " ideal model delta sigma weight residual 108.00 76.10 31.90 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CE LYS B 5 " pdb=" CD LYS B 5 " pdb=" HD2 LYS B 5 " ideal model delta sigma weight residual 108.00 76.21 31.79 3.00e+00 1.11e-01 1.12e+02 angle pdb=" CE LYS C 5 " pdb=" CD LYS C 5 " pdb=" HD2 LYS C 5 " ideal model delta sigma weight residual 108.00 76.23 31.77 3.00e+00 1.11e-01 1.12e+02 angle pdb=" CE LYS D 5 " pdb=" CD LYS D 5 " pdb=" HD2 LYS D 5 " ideal model delta sigma weight residual 108.00 76.27 31.73 3.00e+00 1.11e-01 1.12e+02 ... (remaining 58451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 14391 17.88 - 35.77: 978 35.77 - 53.65: 264 53.65 - 71.54: 74 71.54 - 89.42: 7 Dihedral angle restraints: 15714 sinusoidal: 8583 harmonic: 7131 Sorted by residual: dihedral pdb=" CB CYS D 127 " pdb=" SG CYS D 127 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 135.24 -42.24 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CB CYS F 127 " pdb=" SG CYS F 127 " pdb=" SG CYS F 141 " pdb=" CB CYS F 141 " ideal model delta sinusoidal sigma weight residual 93.00 134.01 -41.01 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " pdb=" SG CYS C 141 " pdb=" CB CYS C 141 " ideal model delta sinusoidal sigma weight residual 93.00 133.48 -40.48 1 1.00e+01 1.00e-02 2.30e+01 ... (remaining 15711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.290: 2587 0.290 - 0.579: 20 0.579 - 0.869: 0 0.869 - 1.159: 0 1.159 - 1.448: 5 Chirality restraints: 2612 Sorted by residual: chirality pdb=" CB VAL E 68 " pdb=" CA VAL E 68 " pdb=" CG1 VAL E 68 " pdb=" CG2 VAL E 68 " both_signs ideal model delta sigma weight residual False -2.63 -1.18 -1.45 2.00e-01 2.50e+01 5.24e+01 chirality pdb=" CB VAL F 68 " pdb=" CA VAL F 68 " pdb=" CG1 VAL F 68 " pdb=" CG2 VAL F 68 " both_signs ideal model delta sigma weight residual False -2.63 -1.18 -1.44 2.00e-01 2.50e+01 5.22e+01 chirality pdb=" CB VAL D 68 " pdb=" CA VAL D 68 " pdb=" CG1 VAL D 68 " pdb=" CG2 VAL D 68 " both_signs ideal model delta sigma weight residual False -2.63 -1.19 -1.44 2.00e-01 2.50e+01 5.21e+01 ... (remaining 2609 not shown) Planarity restraints: 4659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 279 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.67e+00 pdb=" C ILE F 279 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE F 279 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE F 280 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 304 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO D 305 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 305 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 305 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 304 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO E 305 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 305 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 305 " 0.018 5.00e-02 4.00e+02 ... (remaining 4656 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1310 2.18 - 2.79: 62667 2.79 - 3.39: 86336 3.39 - 4.00: 111371 4.00 - 4.60: 174169 Nonbonded interactions: 435853 Sorted by model distance: nonbonded pdb="HH21 ARG B 418 " pdb=" OD1 ASN B 422 " model vdw 1.576 2.450 nonbonded pdb=" OE1 GLU C 44 " pdb=" H GLU C 44 " model vdw 1.601 2.450 nonbonded pdb=" OE1 GLU B 237 " pdb=" HG SER B 240 " model vdw 1.620 2.450 nonbonded pdb=" HD3 LYS F 5 " pdb=" HE2 LYS F 5 " model vdw 1.642 1.952 nonbonded pdb=" O ILE B 463 " pdb=" HG SER B 466 " model vdw 1.642 2.450 ... (remaining 435848 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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=1.00 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: 1.670 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: 0.160 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.680 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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 0.059 16700 Z= 0.266 Angle : 0.715 10.986 22800 Z= 0.321 Chirality : 0.082 1.448 2612 Planarity : 0.003 0.040 2793 Dihedral : 13.334 89.419 6371 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.39 % Allowed : 9.46 % Favored : 90.15 % 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: 1.78 (0.19), residues: 1945 helix: 3.20 (0.17), residues: 805 sheet: -0.12 (0.24), residues: 450 loop : -0.36 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 418 TYR 0.008 0.001 TYR B 92 PHE 0.011 0.001 PHE F 274 TRP 0.010 0.001 TRP D 437 HIS 0.007 0.001 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00563 (16668) covalent geometry : angle 0.71041 (22716) SS BOND : bond 0.00623 ( 12) SS BOND : angle 1.47046 ( 24) hydrogen bonds : bond 0.13634 ( 845) hydrogen bonds : angle 5.94197 ( 2775) link_BETA1-4 : bond 0.00093 ( 5) link_BETA1-4 : angle 0.33373 ( 15) link_NAG-ASN : bond 0.00216 ( 15) link_NAG-ASN : angle 1.71007 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 MET cc_start: 0.8801 (ttp) cc_final: 0.8517 (ttt) REVERT: C 246 LEU cc_start: 0.9570 (tp) cc_final: 0.9365 (tt) outliers start: 7 outliers final: 6 residues processed: 121 average time/residue: 0.2388 time to fit residues: 46.4569 Evaluate side-chains 115 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.096423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.069489 restraints weight = 148278.256| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.35 r_work: 0.3185 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.0587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16700 Z= 0.162 Angle : 0.570 10.950 22800 Z= 0.292 Chirality : 0.074 1.434 2612 Planarity : 0.004 0.041 2793 Dihedral : 8.119 80.926 2658 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.84 % Allowed : 9.07 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.19), residues: 1945 helix: 3.42 (0.16), residues: 790 sheet: -0.17 (0.24), residues: 450 loop : -0.51 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 418 TYR 0.007 0.001 TYR E 187 PHE 0.007 0.001 PHE E 99 TRP 0.008 0.001 TRP E 437 HIS 0.004 0.001 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00360 (16668) covalent geometry : angle 0.56215 (22716) SS BOND : bond 0.00694 ( 12) SS BOND : angle 1.63988 ( 24) hydrogen bonds : bond 0.04906 ( 845) hydrogen bonds : angle 4.80326 ( 2775) link_BETA1-4 : bond 0.00198 ( 5) link_BETA1-4 : angle 0.92309 ( 15) link_NAG-ASN : bond 0.00187 ( 15) link_NAG-ASN : angle 1.90868 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 MET cc_start: 0.8869 (ttp) cc_final: 0.8525 (ttt) REVERT: E 304 MET cc_start: 0.6826 (tpp) cc_final: 0.6507 (tpp) REVERT: F 465 MET cc_start: 0.8423 (tpp) cc_final: 0.7807 (tmm) outliers start: 15 outliers final: 11 residues processed: 123 average time/residue: 0.2394 time to fit residues: 47.7307 Evaluate side-chains 118 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 269 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 191 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 189 optimal weight: 20.0000 chunk 28 optimal weight: 0.5980 chunk 149 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.097033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.069204 restraints weight = 147653.187| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.49 r_work: 0.3137 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16700 Z= 0.125 Angle : 0.545 10.907 22800 Z= 0.274 Chirality : 0.073 1.425 2612 Planarity : 0.003 0.042 2793 Dihedral : 7.040 81.712 2658 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.18 % Allowed : 9.29 % Favored : 89.53 % 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: 1.84 (0.19), residues: 1945 helix: 3.32 (0.16), residues: 820 sheet: -0.19 (0.24), residues: 460 loop : -0.44 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 418 TYR 0.005 0.001 TYR C 92 PHE 0.006 0.001 PHE E 99 TRP 0.007 0.001 TRP E 307 HIS 0.004 0.000 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00284 (16668) covalent geometry : angle 0.53696 (22716) SS BOND : bond 0.00670 ( 12) SS BOND : angle 1.49401 ( 24) hydrogen bonds : bond 0.04389 ( 845) hydrogen bonds : angle 4.45643 ( 2775) link_BETA1-4 : bond 0.00222 ( 5) link_BETA1-4 : angle 1.00055 ( 15) link_NAG-ASN : bond 0.00085 ( 15) link_NAG-ASN : angle 1.89665 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 465 MET cc_start: 0.8505 (tpp) cc_final: 0.7904 (tmm) outliers start: 21 outliers final: 11 residues processed: 124 average time/residue: 0.2565 time to fit residues: 51.4068 Evaluate side-chains 117 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 269 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 160 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.095878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.069594 restraints weight = 146719.925| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.32 r_work: 0.3180 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16700 Z= 0.188 Angle : 0.582 11.962 22800 Z= 0.293 Chirality : 0.073 1.442 2612 Planarity : 0.004 0.050 2793 Dihedral : 6.670 82.845 2656 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.01 % Allowed : 10.08 % Favored : 88.91 % 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: 1.77 (0.19), residues: 1945 helix: 3.26 (0.16), residues: 825 sheet: -0.29 (0.25), residues: 440 loop : -0.46 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 423 TYR 0.009 0.001 TYR E 187 PHE 0.011 0.001 PHE B 252 TRP 0.010 0.001 TRP D 437 HIS 0.006 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00429 (16668) covalent geometry : angle 0.57209 (22716) SS BOND : bond 0.00697 ( 12) SS BOND : angle 1.60662 ( 24) hydrogen bonds : bond 0.04117 ( 845) hydrogen bonds : angle 4.33896 ( 2775) link_BETA1-4 : bond 0.00099 ( 5) link_BETA1-4 : angle 1.09766 ( 15) link_NAG-ASN : bond 0.00316 ( 15) link_NAG-ASN : angle 2.08481 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 278 MET cc_start: 0.9028 (mmm) cc_final: 0.8528 (mmt) outliers start: 18 outliers final: 12 residues processed: 124 average time/residue: 0.2474 time to fit residues: 49.8939 Evaluate side-chains 118 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 269 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.095347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.069063 restraints weight = 147814.818| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.30 r_work: 0.3142 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16700 Z= 0.194 Angle : 0.571 10.961 22800 Z= 0.289 Chirality : 0.074 1.440 2612 Planarity : 0.004 0.042 2793 Dihedral : 6.432 83.200 2652 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.01 % Allowed : 10.25 % Favored : 88.74 % 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: 1.72 (0.19), residues: 1945 helix: 3.26 (0.16), residues: 820 sheet: -0.41 (0.25), residues: 440 loop : -0.43 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 423 TYR 0.009 0.001 TYR C 92 PHE 0.011 0.001 PHE B 252 TRP 0.008 0.001 TRP E 307 HIS 0.005 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00440 (16668) covalent geometry : angle 0.56227 (22716) SS BOND : bond 0.00721 ( 12) SS BOND : angle 1.69578 ( 24) hydrogen bonds : bond 0.04042 ( 845) hydrogen bonds : angle 4.29705 ( 2775) link_BETA1-4 : bond 0.00251 ( 5) link_BETA1-4 : angle 1.00318 ( 15) link_NAG-ASN : bond 0.00210 ( 15) link_NAG-ASN : angle 1.94266 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 237 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7723 (mm-30) REVERT: D 304 MET cc_start: 0.5832 (tpp) cc_final: 0.5102 (tpp) outliers start: 18 outliers final: 15 residues processed: 125 average time/residue: 0.2495 time to fit residues: 50.5110 Evaluate side-chains 122 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 269 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 103 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 184 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 170 ASN E 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.094351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.068020 restraints weight = 147581.498| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.30 r_work: 0.3122 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16700 Z= 0.232 Angle : 0.588 10.999 22800 Z= 0.299 Chirality : 0.074 1.443 2612 Planarity : 0.004 0.040 2793 Dihedral : 6.455 83.914 2652 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.30 % Allowed : 10.53 % Favored : 88.18 % 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: 1.57 (0.19), residues: 1945 helix: 3.22 (0.16), residues: 820 sheet: -0.61 (0.25), residues: 450 loop : -0.52 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 206 TYR 0.011 0.001 TYR E 187 PHE 0.009 0.001 PHE B 99 TRP 0.008 0.001 TRP E 437 HIS 0.004 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00529 (16668) covalent geometry : angle 0.57913 (22716) SS BOND : bond 0.00710 ( 12) SS BOND : angle 1.73988 ( 24) hydrogen bonds : bond 0.03965 ( 845) hydrogen bonds : angle 4.33250 ( 2775) link_BETA1-4 : bond 0.00061 ( 5) link_BETA1-4 : angle 1.04587 ( 15) link_NAG-ASN : bond 0.00380 ( 15) link_NAG-ASN : angle 2.03657 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 260 MET cc_start: 0.8785 (tpp) cc_final: 0.7863 (mmm) outliers start: 23 outliers final: 19 residues processed: 120 average time/residue: 0.2417 time to fit residues: 46.8858 Evaluate side-chains 124 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 269 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 186 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 47 optimal weight: 0.0670 chunk 149 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.095211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.069104 restraints weight = 145327.445| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.25 r_work: 0.3148 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16700 Z= 0.105 Angle : 0.546 10.767 22800 Z= 0.272 Chirality : 0.073 1.414 2612 Planarity : 0.003 0.040 2793 Dihedral : 5.946 84.044 2652 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.84 % Allowed : 10.92 % Favored : 88.23 % 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: 1.75 (0.19), residues: 1945 helix: 3.38 (0.16), residues: 820 sheet: -0.51 (0.24), residues: 460 loop : -0.44 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 7 TYR 0.006 0.001 TYR F 117 PHE 0.008 0.001 PHE B 252 TRP 0.010 0.001 TRP D 437 HIS 0.002 0.000 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00242 (16668) covalent geometry : angle 0.53865 (22716) SS BOND : bond 0.00725 ( 12) SS BOND : angle 1.52521 ( 24) hydrogen bonds : bond 0.03788 ( 845) hydrogen bonds : angle 4.15152 ( 2775) link_BETA1-4 : bond 0.00365 ( 5) link_BETA1-4 : angle 0.85864 ( 15) link_NAG-ASN : bond 0.00113 ( 15) link_NAG-ASN : angle 1.76460 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 288 THR cc_start: 0.8743 (m) cc_final: 0.8479 (p) outliers start: 15 outliers final: 14 residues processed: 121 average time/residue: 0.2351 time to fit residues: 46.1882 Evaluate side-chains 121 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 269 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 128 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 190 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.094811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.068507 restraints weight = 146967.882| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.29 r_work: 0.3135 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16700 Z= 0.152 Angle : 0.556 10.884 22800 Z= 0.278 Chirality : 0.073 1.420 2612 Planarity : 0.003 0.036 2793 Dihedral : 5.844 84.395 2652 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.79 % Allowed : 11.26 % Favored : 87.95 % 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: 1.73 (0.19), residues: 1945 helix: 3.39 (0.16), residues: 820 sheet: -0.56 (0.24), residues: 450 loop : -0.47 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 7 TYR 0.007 0.001 TYR E 187 PHE 0.008 0.001 PHE B 99 TRP 0.009 0.001 TRP E 437 HIS 0.002 0.000 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00350 (16668) covalent geometry : angle 0.54759 (22716) SS BOND : bond 0.00703 ( 12) SS BOND : angle 1.55482 ( 24) hydrogen bonds : bond 0.03731 ( 845) hydrogen bonds : angle 4.14224 ( 2775) link_BETA1-4 : bond 0.00175 ( 5) link_BETA1-4 : angle 1.02126 ( 15) link_NAG-ASN : bond 0.00195 ( 15) link_NAG-ASN : angle 1.91515 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 260 MET cc_start: 0.8757 (tpp) cc_final: 0.7879 (mmm) outliers start: 14 outliers final: 13 residues processed: 120 average time/residue: 0.2577 time to fit residues: 50.1076 Evaluate side-chains 120 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 269 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 20 optimal weight: 1.9990 chunk 191 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 188 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.094900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.068674 restraints weight = 145993.981| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.27 r_work: 0.3133 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16700 Z= 0.142 Angle : 0.556 10.847 22800 Z= 0.277 Chirality : 0.073 1.419 2612 Planarity : 0.003 0.041 2793 Dihedral : 5.701 84.683 2652 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.90 % Allowed : 11.15 % Favored : 87.95 % 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: 1.75 (0.19), residues: 1945 helix: 3.41 (0.16), residues: 820 sheet: -0.54 (0.25), residues: 450 loop : -0.47 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 423 TYR 0.006 0.001 TYR F 117 PHE 0.007 0.001 PHE E 99 TRP 0.011 0.001 TRP D 437 HIS 0.002 0.000 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00327 (16668) covalent geometry : angle 0.54836 (22716) SS BOND : bond 0.00746 ( 12) SS BOND : angle 1.60598 ( 24) hydrogen bonds : bond 0.03651 ( 845) hydrogen bonds : angle 4.10064 ( 2775) link_BETA1-4 : bond 0.00322 ( 5) link_BETA1-4 : angle 0.93723 ( 15) link_NAG-ASN : bond 0.00099 ( 15) link_NAG-ASN : angle 1.78404 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 260 MET cc_start: 0.8791 (tpp) cc_final: 0.7888 (mmm) REVERT: B 418 ARG cc_start: 0.7934 (tpm170) cc_final: 0.7713 (tpm170) outliers start: 16 outliers final: 12 residues processed: 121 average time/residue: 0.2620 time to fit residues: 49.7606 Evaluate side-chains 120 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 86 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 176 optimal weight: 0.0020 chunk 148 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.095317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069271 restraints weight = 147008.647| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.28 r_work: 0.3151 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16700 Z= 0.103 Angle : 0.550 10.742 22800 Z= 0.270 Chirality : 0.072 1.407 2612 Planarity : 0.003 0.036 2793 Dihedral : 5.346 84.791 2652 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.62 % Allowed : 11.60 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.19), residues: 1945 helix: 3.47 (0.16), residues: 820 sheet: -0.38 (0.25), residues: 440 loop : -0.39 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 9 TYR 0.006 0.001 TYR F 117 PHE 0.006 0.001 PHE C 274 TRP 0.009 0.001 TRP E 437 HIS 0.001 0.000 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00242 (16668) covalent geometry : angle 0.54329 (22716) SS BOND : bond 0.00708 ( 12) SS BOND : angle 1.41714 ( 24) hydrogen bonds : bond 0.03571 ( 845) hydrogen bonds : angle 4.01738 ( 2775) link_BETA1-4 : bond 0.00418 ( 5) link_BETA1-4 : angle 0.97005 ( 15) link_NAG-ASN : bond 0.00075 ( 15) link_NAG-ASN : angle 1.74748 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 418 ARG cc_start: 0.7906 (tpm170) cc_final: 0.7690 (tpm170) REVERT: E 288 THR cc_start: 0.8798 (m) cc_final: 0.8521 (p) REVERT: F 40 MET cc_start: 0.9016 (mmm) cc_final: 0.8767 (mmp) outliers start: 11 outliers final: 9 residues processed: 119 average time/residue: 0.2437 time to fit residues: 45.9427 Evaluate side-chains 117 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 17 optimal weight: 0.0070 chunk 175 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 155 optimal weight: 10.0000 chunk 69 optimal weight: 0.2980 chunk 192 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.095839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.069719 restraints weight = 146991.093| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.31 r_work: 0.3170 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16700 Z= 0.097 Angle : 0.540 10.793 22800 Z= 0.266 Chirality : 0.072 1.407 2612 Planarity : 0.003 0.038 2793 Dihedral : 4.933 84.927 2650 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.51 % Allowed : 11.82 % Favored : 87.67 % 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: 1.90 (0.19), residues: 1945 helix: 3.46 (0.16), residues: 825 sheet: -0.34 (0.25), residues: 440 loop : -0.42 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 9 TYR 0.010 0.001 TYR D 209 PHE 0.005 0.001 PHE E 452 TRP 0.010 0.001 TRP D 437 HIS 0.001 0.000 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00229 (16668) covalent geometry : angle 0.53322 (22716) SS BOND : bond 0.00795 ( 12) SS BOND : angle 1.46936 ( 24) hydrogen bonds : bond 0.03468 ( 845) hydrogen bonds : angle 3.94438 ( 2775) link_BETA1-4 : bond 0.00297 ( 5) link_BETA1-4 : angle 0.92103 ( 15) link_NAG-ASN : bond 0.00080 ( 15) link_NAG-ASN : angle 1.73132 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7583.03 seconds wall clock time: 129 minutes 18.92 seconds (7758.92 seconds total)