Starting phenix.real_space_refine on Thu Aug 6 00:38:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bxb_16314/08_2026/8bxb_16314.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bxb_16314/08_2026/8bxb_16314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8bxb_16314/08_2026/8bxb_16314.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bxb_16314/08_2026/8bxb_16314.cif" model { file = "/net/cci-nas-00/data/ceres_data/8bxb_16314/08_2026/8bxb_16314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bxb_16314/08_2026/8bxb_16314.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bxb_16314/08_2026/8bxb_16314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bxb_16314/08_2026/8bxb_16314.map" } resolution = 3.9 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= 0.001 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 76 5.16 5 C 8320 2.51 5 N 2032 2.21 5 O 2119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12547 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2496 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 102 Chain: "B" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2499 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2493 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 102 Chain: "D" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2492 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 102 Chain: "E" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2493 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 102 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.68, per 1000 atoms: 0.21 Number of scatterers: 12547 At special positions: 0 Unit cell: (91.152, 91.152, 121.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 76 16.00 O 2119 8.00 N 2032 7.00 C 8320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.49 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.49 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.49 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 152 " distance=2.49 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 NAG-ASN " NAG A 501 " - " ASN A 167 " " NAG B 501 " - " ASN B 167 " " NAG C 501 " - " ASN C 167 " " NAG D 501 " - " ASN D 167 " " NAG E 501 " - " ASN E 167 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 407.1 milliseconds 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3130 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 39.6% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.910A pdb=" N SER A 83 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 95 removed outlier: 3.546A pdb=" N ILE A 95 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 removed outlier: 3.764A pdb=" N ARG A 144 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 225 through 239 Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.640A pdb=" N LYS A 247 " --> pdb=" O PRO A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 279 through 307 removed outlier: 3.600A pdb=" N MET A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 440 Processing helix chain 'B' and resid 13 through 19 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.911A pdb=" N SER B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 95 removed outlier: 3.545A pdb=" N ILE B 95 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.765A pdb=" N ARG B 144 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 239 Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.640A pdb=" N LYS B 247 " --> pdb=" O PRO B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 271 Processing helix chain 'B' and resid 279 through 307 removed outlier: 3.601A pdb=" N MET B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 440 Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.911A pdb=" N SER C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.545A pdb=" N ILE C 95 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 145 removed outlier: 3.764A pdb=" N ARG C 144 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 225 through 239 Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.641A pdb=" N LYS C 247 " --> pdb=" O PRO C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 279 through 307 removed outlier: 3.601A pdb=" N MET C 307 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 440 Processing helix chain 'D' and resid 13 through 19 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.910A pdb=" N SER D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 removed outlier: 3.546A pdb=" N ILE D 95 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 removed outlier: 3.765A pdb=" N ARG D 144 " --> pdb=" O ASP D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 239 Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.640A pdb=" N LYS D 247 " --> pdb=" O PRO D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 271 Processing helix chain 'D' and resid 279 through 307 removed outlier: 3.600A pdb=" N MET D 307 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 440 Processing helix chain 'E' and resid 13 through 19 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.911A pdb=" N SER E 83 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.545A pdb=" N ILE E 95 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 145 removed outlier: 3.764A pdb=" N ARG E 144 " --> pdb=" O ASP E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 225 Processing helix chain 'E' and resid 225 through 239 Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 243 through 247 removed outlier: 3.639A pdb=" N LYS E 247 " --> pdb=" O PRO E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 279 through 307 removed outlier: 3.600A pdb=" N MET E 307 " --> pdb=" O ILE E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 440 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL A 126 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 70 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL A 126 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 70 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL A 59 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP A 52 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N THR A 61 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN A 63 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.780A pdb=" N GLY A 207 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG A 194 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 209 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY A 211 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL B 126 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP B 70 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL B 126 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP B 70 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL B 59 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP B 52 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR B 61 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN B 63 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.780A pdb=" N GLY B 207 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG B 194 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE B 209 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY B 211 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL C 126 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP C 70 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL C 126 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP C 70 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL C 59 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP C 52 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR C 61 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL C 50 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN C 63 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 87 through 90 Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.781A pdb=" N GLY C 207 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG C 194 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE C 209 " --> pdb=" O PRO C 192 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY C 211 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL D 126 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 70 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL D 126 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 70 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL D 59 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP D 52 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR D 61 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN D 63 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 87 through 90 Processing sheet with id=AB7, first strand: chain 'D' and resid 100 through 102 removed outlier: 6.780A pdb=" N GLY D 207 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG D 194 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE D 209 " --> pdb=" O PRO D 192 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY D 211 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 125 through 126 removed outlier: 3.659A pdb=" N VAL E 126 " --> pdb=" O TRP E 70 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 70 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 125 through 126 removed outlier: 3.659A pdb=" N VAL E 126 " --> pdb=" O TRP E 70 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 70 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL E 59 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP E 52 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR E 61 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL E 50 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN E 63 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 87 through 90 Processing sheet with id=AC2, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.781A pdb=" N GLY E 207 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG E 194 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE E 209 " --> pdb=" O PRO E 192 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY E 211 " --> pdb=" O VAL E 190 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1650 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: 1.59 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2498 1.33 - 1.45: 3056 1.45 - 1.57: 7181 1.57 - 1.69: 0 1.69 - 1.81: 133 Bond restraints: 12868 Sorted by residual: bond pdb=" N VAL A 113 " pdb=" CA VAL A 113 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.19e-02 7.06e+03 9.95e+00 bond pdb=" N VAL C 114 " pdb=" CA VAL C 114 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.95e+00 bond pdb=" N SER A 109 " pdb=" CA SER A 109 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.27e-02 6.20e+03 7.36e+00 bond pdb=" N ARG A 171 " pdb=" CA ARG A 171 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 6.90e+00 bond pdb=" N VAL C 113 " pdb=" CA VAL C 113 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.64e+00 ... (remaining 12863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 17225 2.24 - 4.49: 369 4.49 - 6.73: 41 6.73 - 8.98: 23 8.98 - 11.22: 1 Bond angle restraints: 17659 Sorted by residual: angle pdb=" N LEU C 285 " pdb=" CA LEU C 285 " pdb=" C LEU C 285 " ideal model delta sigma weight residual 111.82 100.60 11.22 1.16e+00 7.43e-01 9.36e+01 angle pdb=" CA LEU B 285 " pdb=" C LEU B 285 " pdb=" N ALA B 286 " ideal model delta sigma weight residual 118.14 110.15 7.99 1.31e+00 5.83e-01 3.72e+01 angle pdb=" CA LEU E 285 " pdb=" C LEU E 285 " pdb=" N ALA E 286 " ideal model delta sigma weight residual 118.14 110.40 7.74 1.31e+00 5.83e-01 3.49e+01 angle pdb=" N ALA A 286 " pdb=" CA ALA A 286 " pdb=" C ALA A 286 " ideal model delta sigma weight residual 111.82 105.03 6.79 1.16e+00 7.43e-01 3.43e+01 angle pdb=" N ALA E 286 " pdb=" CA ALA E 286 " pdb=" C ALA E 286 " ideal model delta sigma weight residual 112.23 105.08 7.15 1.26e+00 6.30e-01 3.22e+01 ... (remaining 17654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.98: 6408 11.98 - 23.95: 643 23.95 - 35.93: 209 35.93 - 47.90: 112 47.90 - 59.88: 47 Dihedral angle restraints: 7419 sinusoidal: 2574 harmonic: 4845 Sorted by residual: dihedral pdb=" CB CYS C 138 " pdb=" SG CYS C 138 " pdb=" SG CYS C 152 " pdb=" CB CYS C 152 " ideal model delta sinusoidal sigma weight residual 93.00 147.07 -54.07 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CB CYS D 138 " pdb=" SG CYS D 138 " pdb=" SG CYS D 152 " pdb=" CB CYS D 152 " ideal model delta sinusoidal sigma weight residual 93.00 147.05 -54.05 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual 93.00 147.03 -54.03 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 7416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1651 0.054 - 0.109: 373 0.109 - 0.163: 133 0.163 - 0.217: 12 0.217 - 0.272: 6 Chirality restraints: 2175 Sorted by residual: chirality pdb=" CA VAL E 114 " pdb=" N VAL E 114 " pdb=" C VAL E 114 " pdb=" CB VAL E 114 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL E 288 " pdb=" CA VAL E 288 " pdb=" CG1 VAL E 288 " pdb=" CG2 VAL E 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB VAL A 288 " pdb=" CA VAL A 288 " pdb=" CG1 VAL A 288 " pdb=" CG2 VAL A 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 2172 not shown) Planarity restraints: 2126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 285 " 0.027 2.00e-02 2.50e+03 5.83e-02 3.40e+01 pdb=" C LEU B 285 " -0.101 2.00e-02 2.50e+03 pdb=" O LEU B 285 " 0.040 2.00e-02 2.50e+03 pdb=" N ALA B 286 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 286 " 0.028 2.00e-02 2.50e+03 5.74e-02 3.30e+01 pdb=" C ALA D 286 " -0.099 2.00e-02 2.50e+03 pdb=" O ALA D 286 " 0.038 2.00e-02 2.50e+03 pdb=" N TYR D 287 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 285 " -0.026 2.00e-02 2.50e+03 5.58e-02 3.11e+01 pdb=" C LEU E 285 " 0.096 2.00e-02 2.50e+03 pdb=" O LEU E 285 " -0.038 2.00e-02 2.50e+03 pdb=" N ALA E 286 " -0.033 2.00e-02 2.50e+03 ... (remaining 2123 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2836 2.78 - 3.31: 10902 3.31 - 3.84: 20960 3.84 - 4.37: 22511 4.37 - 4.90: 39189 Nonbonded interactions: 96398 Sorted by model distance: nonbonded pdb=" CD1 LEU D 170 " pdb=" O ARG D 171 " model vdw 2.256 3.460 nonbonded pdb=" CD1 LEU C 170 " pdb=" O ARG C 171 " model vdw 2.259 3.460 nonbonded pdb=" OD1 ASN A 78 " pdb=" OG SER A 80 " model vdw 2.318 3.040 nonbonded pdb=" OD1 ASN D 78 " pdb=" OG SER D 80 " model vdw 2.319 3.040 nonbonded pdb=" OD1 ASN B 78 " pdb=" OG SER B 80 " model vdw 2.319 3.040 ... (remaining 96393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 304 or (resid 305 and (name N or n \ ame CA or name C or name O or name CB )) or resid 306 through 501)) selection = (chain 'B' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 269 or (resid 270 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name NE )) or res \ id 271 through 306 or (resid 307 and (name N or name CA or name C or name O or n \ ame CB )) or resid 414 through 501)) selection = (chain 'C' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 501)) selection = chain 'D' selection = (chain 'E' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 501)) } 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 group one per residue 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: 6.460 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.450 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 : 0.009 0.463 12877 Z= 0.468 Angle : 0.963 33.763 17682 Z= 0.548 Chirality : 0.055 0.272 2175 Planarity : 0.006 0.098 2121 Dihedral : 13.542 59.880 4277 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.85 % Favored : 96.09 % Rotamer: Outliers : 5.55 % Allowed : 14.10 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.59 (0.19), residues: 1610 helix: -1.63 (0.18), residues: 535 sheet: -1.19 (0.28), residues: 410 loop : -1.98 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 270 TYR 0.014 0.002 TYR A 287 PHE 0.012 0.001 PHE B 289 TRP 0.010 0.001 TRP E 159 HIS 0.005 0.001 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.23 (12868) covalent geometry : angle 0.77856 / 0.48 (17659) SS BOND : bond 0.46123 / 21.22 ( 4) SS BOND : angle 26.70697 / 15.62 ( 8) hydrogen bonds : bond 0.15526 / 10.89 ( 580) hydrogen bonds : angle 6.18963 / 4.26 ( 1650) link_NAG-ASN : bond 0.00266 / 0.14 ( 5) link_NAG-ASN : angle 0.28934 / 0.16 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 294 time to evaluate : 0.480 Fit side-chains REVERT: A 104 ASN cc_start: 0.7294 (OUTLIER) cc_final: 0.6791 (p0) REVERT: A 264 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8195 (tt) REVERT: A 265 MET cc_start: 0.8529 (ttp) cc_final: 0.8270 (ttt) REVERT: A 271 MET cc_start: 0.7761 (tmm) cc_final: 0.7490 (tmm) REVERT: B 17 LEU cc_start: 0.8255 (tp) cc_final: 0.7926 (tp) REVERT: B 264 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8260 (mt) REVERT: B 265 MET cc_start: 0.8577 (ttp) cc_final: 0.8194 (ttp) REVERT: B 271 MET cc_start: 0.7555 (tmm) cc_final: 0.7317 (tmm) REVERT: C 21 ILE cc_start: 0.9029 (tp) cc_final: 0.8672 (tt) REVERT: C 87 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8433 (mtpt) REVERT: C 271 MET cc_start: 0.7734 (tmm) cc_final: 0.7467 (tmm) REVERT: D 21 ILE cc_start: 0.9018 (tp) cc_final: 0.8720 (tt) REVERT: D 104 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.6775 (p0) REVERT: D 264 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8191 (mt) REVERT: D 265 MET cc_start: 0.8430 (ttp) cc_final: 0.8104 (ttm) REVERT: D 271 MET cc_start: 0.7810 (tmm) cc_final: 0.7499 (tmm) REVERT: E 21 ILE cc_start: 0.9084 (tp) cc_final: 0.8711 (tt) REVERT: E 239 MET cc_start: 0.7409 (ttp) cc_final: 0.7156 (ttt) REVERT: E 264 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8254 (mt) REVERT: E 265 MET cc_start: 0.8441 (ttp) cc_final: 0.8111 (ttp) REVERT: E 271 MET cc_start: 0.7560 (tmm) cc_final: 0.7199 (tmm) outliers start: 70 outliers final: 8 residues processed: 354 average time/residue: 0.0682 time to fit residues: 39.2718 Evaluate side-chains 237 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 264 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 HIS C 58 HIS D 58 HIS E 58 HIS E 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.141510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112158 restraints weight = 22638.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115941 restraints weight = 14222.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118456 restraints weight = 10454.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120453 restraints weight = 8517.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121625 restraints weight = 7327.304| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12877 Z= 0.136 Angle : 0.555 5.742 17682 Z= 0.285 Chirality : 0.043 0.145 2175 Planarity : 0.004 0.030 2121 Dihedral : 4.951 56.837 1795 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.68 % Allowed : 18.70 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.53 (0.21), residues: 1610 helix: 0.02 (0.21), residues: 540 sheet: -0.76 (0.28), residues: 400 loop : -1.99 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 194 TYR 0.016 0.001 TYR B 287 PHE 0.019 0.001 PHE D 298 TRP 0.010 0.001 TRP A 70 HIS 0.004 0.001 HIS E 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (12868) covalent geometry : angle 0.55348 / 0.28 (17659) SS BOND : bond 0.00064 / 0.03 ( 4) SS BOND : angle 1.70097 / 1.00 ( 8) hydrogen bonds : bond 0.03921 / 2.71 ( 580) hydrogen bonds : angle 4.52135 / 3.15 ( 1650) link_NAG-ASN : bond 0.00171 / 0.09 ( 5) link_NAG-ASN : angle 1.23405 / 0.76 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 247 time to evaluate : 0.383 Fit side-chains REVERT: A 104 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7910 (p0) REVERT: A 265 MET cc_start: 0.8608 (ttp) cc_final: 0.8317 (ttt) REVERT: A 271 MET cc_start: 0.7739 (tmm) cc_final: 0.7349 (tmm) REVERT: A 275 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8101 (mt) REVERT: B 100 ILE cc_start: 0.8997 (mt) cc_final: 0.8601 (tp) REVERT: B 265 MET cc_start: 0.8479 (ttp) cc_final: 0.8237 (ttp) REVERT: B 271 MET cc_start: 0.7500 (tmm) cc_final: 0.7135 (tmm) REVERT: B 275 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8100 (mt) REVERT: C 21 ILE cc_start: 0.9235 (tp) cc_final: 0.8821 (tt) REVERT: C 87 LYS cc_start: 0.8753 (mtpt) cc_final: 0.8526 (mtpt) REVERT: C 127 MET cc_start: 0.8375 (mtp) cc_final: 0.8058 (mtp) REVERT: C 196 GLN cc_start: 0.8001 (mp10) cc_final: 0.7760 (mp10) REVERT: C 271 MET cc_start: 0.7869 (tmm) cc_final: 0.7667 (tmm) REVERT: C 275 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8070 (mt) REVERT: D 21 ILE cc_start: 0.9301 (tp) cc_final: 0.8922 (tt) REVERT: D 23 HIS cc_start: 0.8126 (OUTLIER) cc_final: 0.7846 (t-170) REVERT: D 104 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7794 (p0) REVERT: D 196 GLN cc_start: 0.8018 (mp10) cc_final: 0.7777 (mp10) REVERT: D 275 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8148 (mt) REVERT: D 291 MET cc_start: 0.8722 (tpp) cc_final: 0.8438 (tpp) REVERT: E 17 LEU cc_start: 0.8746 (tp) cc_final: 0.8479 (tp) REVERT: E 21 ILE cc_start: 0.9268 (tp) cc_final: 0.8892 (tt) REVERT: E 23 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7810 (t-170) REVERT: E 239 MET cc_start: 0.8088 (ttp) cc_final: 0.7725 (ttt) REVERT: E 265 MET cc_start: 0.8376 (ttp) cc_final: 0.8064 (ttp) REVERT: E 271 MET cc_start: 0.7555 (tmm) cc_final: 0.7282 (tmm) REVERT: E 287 TYR cc_start: 0.8052 (t80) cc_final: 0.7583 (t80) outliers start: 59 outliers final: 33 residues processed: 279 average time/residue: 0.0717 time to fit residues: 32.7049 Evaluate side-chains 268 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 23 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 275 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 54 optimal weight: 0.2980 chunk 126 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.139118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109706 restraints weight = 23076.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.113320 restraints weight = 14723.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115912 restraints weight = 10938.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117599 restraints weight = 8922.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118992 restraints weight = 7769.864| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12877 Z= 0.151 Angle : 0.559 8.312 17682 Z= 0.282 Chirality : 0.044 0.151 2175 Planarity : 0.003 0.026 2121 Dihedral : 4.009 18.252 1775 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.91 % Allowed : 20.36 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.16 (0.21), residues: 1610 helix: 0.65 (0.21), residues: 545 sheet: -0.76 (0.28), residues: 410 loop : -1.97 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 16 TYR 0.020 0.001 TYR C 287 PHE 0.016 0.001 PHE E 73 TRP 0.009 0.001 TRP E 185 HIS 0.004 0.001 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (12868) covalent geometry : angle 0.55717 / 0.28 (17659) SS BOND : bond 0.00435 / 0.20 ( 4) SS BOND : angle 1.16690 / 0.69 ( 8) hydrogen bonds : bond 0.03699 / 2.57 ( 580) hydrogen bonds : angle 4.36331 / 3.05 ( 1650) link_NAG-ASN : bond 0.00174 / 0.09 ( 5) link_NAG-ASN : angle 1.30560 / 0.79 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 241 time to evaluate : 0.432 Fit side-chains REVERT: A 104 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7966 (p0) REVERT: A 265 MET cc_start: 0.8559 (ttp) cc_final: 0.8293 (ttt) REVERT: B 100 ILE cc_start: 0.9062 (mt) cc_final: 0.8689 (tp) REVERT: B 138 CYS cc_start: 0.7785 (p) cc_final: 0.7494 (m) REVERT: B 271 MET cc_start: 0.7639 (tmm) cc_final: 0.7249 (tmm) REVERT: C 21 ILE cc_start: 0.9272 (tp) cc_final: 0.8853 (tt) REVERT: C 87 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8563 (mtpt) REVERT: C 100 ILE cc_start: 0.8984 (mt) cc_final: 0.8625 (tp) REVERT: C 196 GLN cc_start: 0.8076 (mp10) cc_final: 0.7791 (mp10) REVERT: C 271 MET cc_start: 0.7771 (tmm) cc_final: 0.7413 (tmm) REVERT: D 21 ILE cc_start: 0.9344 (tp) cc_final: 0.8957 (tt) REVERT: D 23 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7878 (t-170) REVERT: D 100 ILE cc_start: 0.9068 (mt) cc_final: 0.8725 (tp) REVERT: D 104 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7693 (p0) REVERT: D 196 GLN cc_start: 0.8071 (mp10) cc_final: 0.7790 (mp10) REVERT: D 291 MET cc_start: 0.8827 (tpp) cc_final: 0.8592 (tpp) REVERT: E 17 LEU cc_start: 0.8774 (tp) cc_final: 0.8480 (tp) REVERT: E 21 ILE cc_start: 0.9310 (tp) cc_final: 0.8898 (tt) REVERT: E 23 HIS cc_start: 0.8076 (OUTLIER) cc_final: 0.7859 (t-170) REVERT: E 264 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7909 (tt) REVERT: E 265 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7991 (ttp) REVERT: E 271 MET cc_start: 0.7660 (tmm) cc_final: 0.7433 (tmm) outliers start: 62 outliers final: 35 residues processed: 280 average time/residue: 0.0779 time to fit residues: 35.7842 Evaluate side-chains 264 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 23 HIS Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 265 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 96 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.138161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.108770 restraints weight = 22819.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112312 restraints weight = 14618.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.114824 restraints weight = 10915.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116444 restraints weight = 8935.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117806 restraints weight = 7812.226| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12877 Z= 0.143 Angle : 0.552 7.609 17682 Z= 0.280 Chirality : 0.044 0.166 2175 Planarity : 0.003 0.024 2121 Dihedral : 3.986 17.798 1775 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.31 % Allowed : 19.57 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.21), residues: 1610 helix: 0.99 (0.21), residues: 545 sheet: -0.67 (0.28), residues: 410 loop : -2.00 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 270 TYR 0.016 0.001 TYR C 287 PHE 0.013 0.001 PHE D 298 TRP 0.008 0.001 TRP C 185 HIS 0.005 0.001 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (12868) covalent geometry : angle 0.55133 / 0.28 (17659) SS BOND : bond 0.00411 / 0.19 ( 4) SS BOND : angle 0.86827 / 0.51 ( 8) hydrogen bonds : bond 0.03593 / 2.50 ( 580) hydrogen bonds : angle 4.30759 / 3.02 ( 1650) link_NAG-ASN : bond 0.00186 / 0.10 ( 5) link_NAG-ASN : angle 1.19190 / 0.72 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 237 time to evaluate : 0.539 Fit side-chains REVERT: A 21 ILE cc_start: 0.9292 (tp) cc_final: 0.8895 (tt) REVERT: A 104 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7949 (p0) REVERT: A 271 MET cc_start: 0.7879 (tmm) cc_final: 0.7593 (tmm) REVERT: B 21 ILE cc_start: 0.9309 (tp) cc_final: 0.8900 (tt) REVERT: B 100 ILE cc_start: 0.9069 (mt) cc_final: 0.8716 (tp) REVERT: B 271 MET cc_start: 0.7729 (tmm) cc_final: 0.7389 (tmm) REVERT: C 21 ILE cc_start: 0.9283 (tp) cc_final: 0.8909 (tt) REVERT: C 87 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8569 (mtpt) REVERT: C 100 ILE cc_start: 0.8992 (mt) cc_final: 0.8650 (tp) REVERT: C 196 GLN cc_start: 0.8123 (mp10) cc_final: 0.7872 (mp10) REVERT: C 271 MET cc_start: 0.7874 (tmm) cc_final: 0.7579 (tmm) REVERT: D 21 ILE cc_start: 0.9339 (tp) cc_final: 0.8986 (tt) REVERT: D 104 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7689 (p0) REVERT: D 196 GLN cc_start: 0.8126 (mp10) cc_final: 0.7855 (mp10) REVERT: E 17 LEU cc_start: 0.8790 (tp) cc_final: 0.8464 (tp) REVERT: E 21 ILE cc_start: 0.9322 (tp) cc_final: 0.8916 (tt) REVERT: E 127 MET cc_start: 0.8238 (mtt) cc_final: 0.7990 (mtt) REVERT: E 264 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7952 (tt) REVERT: E 265 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7939 (ttp) REVERT: E 271 MET cc_start: 0.7692 (tmm) cc_final: 0.7347 (tmm) REVERT: E 291 MET cc_start: 0.8745 (tpp) cc_final: 0.8516 (tpp) outliers start: 67 outliers final: 39 residues processed: 283 average time/residue: 0.0738 time to fit residues: 34.7019 Evaluate side-chains 268 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 130 optimal weight: 0.0570 chunk 90 optimal weight: 0.4980 chunk 139 optimal weight: 0.0370 chunk 138 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 66 optimal weight: 0.0470 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.140731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.111138 restraints weight = 22751.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.114894 restraints weight = 14376.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.117551 restraints weight = 10625.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119261 restraints weight = 8623.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120733 restraints weight = 7479.949| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12877 Z= 0.103 Angle : 0.551 9.704 17682 Z= 0.275 Chirality : 0.044 0.193 2175 Planarity : 0.003 0.025 2121 Dihedral : 3.905 17.649 1775 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.65 % Allowed : 21.87 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.21), residues: 1610 helix: 1.10 (0.21), residues: 545 sheet: -0.48 (0.28), residues: 410 loop : -1.94 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 249 TYR 0.014 0.001 TYR C 252 PHE 0.011 0.001 PHE A 234 TRP 0.011 0.001 TRP C 77 HIS 0.003 0.001 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (12868) covalent geometry : angle 0.55065 / 0.28 (17659) SS BOND : bond 0.00254 / 0.12 ( 4) SS BOND : angle 0.67285 / 0.39 ( 8) hydrogen bonds : bond 0.03420 / 2.38 ( 580) hydrogen bonds : angle 4.23234 / 2.97 ( 1650) link_NAG-ASN : bond 0.00358 / 0.19 ( 5) link_NAG-ASN : angle 0.65284 / 0.39 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 0.304 Fit side-chains REVERT: A 21 ILE cc_start: 0.9247 (tp) cc_final: 0.8860 (tt) REVERT: A 271 MET cc_start: 0.7916 (tmm) cc_final: 0.7636 (tmm) REVERT: B 21 ILE cc_start: 0.9305 (tp) cc_final: 0.9028 (tt) REVERT: B 271 MET cc_start: 0.7715 (tmm) cc_final: 0.7388 (tmm) REVERT: C 21 ILE cc_start: 0.9227 (tp) cc_final: 0.8880 (tt) REVERT: C 100 ILE cc_start: 0.8867 (mt) cc_final: 0.8549 (tp) REVERT: C 196 GLN cc_start: 0.8117 (mp10) cc_final: 0.7848 (mp10) REVERT: C 271 MET cc_start: 0.7884 (tmm) cc_final: 0.7572 (tmm) REVERT: D 21 ILE cc_start: 0.9318 (tp) cc_final: 0.9002 (tt) REVERT: D 104 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7622 (p0) REVERT: D 196 GLN cc_start: 0.8107 (mp10) cc_final: 0.7831 (mp10) REVERT: D 291 MET cc_start: 0.8658 (tpp) cc_final: 0.8276 (tpp) REVERT: E 21 ILE cc_start: 0.9306 (tp) cc_final: 0.8923 (tt) REVERT: E 127 MET cc_start: 0.7990 (mtt) cc_final: 0.7746 (mtm) REVERT: E 264 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8086 (tt) REVERT: E 265 MET cc_start: 0.8355 (ttp) cc_final: 0.8138 (ttp) REVERT: E 271 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7416 (tmm) outliers start: 46 outliers final: 29 residues processed: 277 average time/residue: 0.0755 time to fit residues: 33.2186 Evaluate side-chains 254 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 271 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 42 optimal weight: 0.3980 chunk 121 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.140844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.112348 restraints weight = 22274.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115785 restraints weight = 14465.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118027 restraints weight = 10859.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119823 restraints weight = 8970.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.120869 restraints weight = 7804.442| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12877 Z= 0.154 Angle : 0.582 8.816 17682 Z= 0.292 Chirality : 0.045 0.174 2175 Planarity : 0.003 0.023 2121 Dihedral : 3.953 17.392 1773 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.04 % Allowed : 22.58 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.21), residues: 1610 helix: 1.13 (0.21), residues: 545 sheet: -0.59 (0.28), residues: 410 loop : -2.01 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 249 TYR 0.017 0.001 TYR C 252 PHE 0.012 0.001 PHE A 298 TRP 0.010 0.001 TRP C 77 HIS 0.003 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (12868) covalent geometry : angle 0.58090 / 0.29 (17659) SS BOND : bond 0.00381 / 0.17 ( 4) SS BOND : angle 0.85316 / 0.49 ( 8) hydrogen bonds : bond 0.03513 / 2.44 ( 580) hydrogen bonds : angle 4.36371 / 3.06 ( 1650) link_NAG-ASN : bond 0.00117 / 0.06 ( 5) link_NAG-ASN : angle 1.37920 / 0.82 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 217 time to evaluate : 0.453 Fit side-chains REVERT: A 21 ILE cc_start: 0.9289 (tp) cc_final: 0.8901 (tt) REVERT: A 271 MET cc_start: 0.8089 (tmm) cc_final: 0.7821 (tmm) REVERT: A 291 MET cc_start: 0.8113 (tpp) cc_final: 0.7798 (tpp) REVERT: B 21 ILE cc_start: 0.9336 (tp) cc_final: 0.9037 (tt) REVERT: B 69 GLU cc_start: 0.7567 (tt0) cc_final: 0.7315 (tt0) REVERT: B 271 MET cc_start: 0.7864 (tmm) cc_final: 0.7577 (tmm) REVERT: C 21 ILE cc_start: 0.9278 (tp) cc_final: 0.8911 (tt) REVERT: C 100 ILE cc_start: 0.9000 (mt) cc_final: 0.8717 (tp) REVERT: C 271 MET cc_start: 0.7951 (tmm) cc_final: 0.7684 (tmm) REVERT: D 21 ILE cc_start: 0.9343 (tp) cc_final: 0.9021 (tt) REVERT: D 104 ASN cc_start: 0.7847 (OUTLIER) cc_final: 0.7467 (p0) REVERT: D 127 MET cc_start: 0.8320 (mtp) cc_final: 0.7873 (mtt) REVERT: D 264 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8246 (tt) REVERT: D 291 MET cc_start: 0.8716 (tpp) cc_final: 0.8319 (tpp) REVERT: E 17 LEU cc_start: 0.8692 (tp) cc_final: 0.8331 (tp) REVERT: E 21 ILE cc_start: 0.9326 (tp) cc_final: 0.8912 (tt) REVERT: E 127 MET cc_start: 0.8383 (mtt) cc_final: 0.8053 (mtt) REVERT: E 264 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8162 (tt) REVERT: E 271 MET cc_start: 0.7850 (tmm) cc_final: 0.7572 (tmm) outliers start: 51 outliers final: 32 residues processed: 251 average time/residue: 0.0787 time to fit residues: 32.2585 Evaluate side-chains 250 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 78 optimal weight: 3.9990 chunk 154 optimal weight: 0.0050 chunk 97 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 130 optimal weight: 0.0010 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.141961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113365 restraints weight = 21907.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116731 restraints weight = 14325.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119149 restraints weight = 10802.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120798 restraints weight = 8883.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.121909 restraints weight = 7751.929| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12877 Z= 0.158 Angle : 0.598 7.878 17682 Z= 0.298 Chirality : 0.045 0.174 2175 Planarity : 0.003 0.022 2121 Dihedral : 3.998 17.313 1773 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.68 % Allowed : 22.11 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.21), residues: 1610 helix: 1.15 (0.21), residues: 545 sheet: -0.57 (0.28), residues: 375 loop : -2.12 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 249 TYR 0.019 0.001 TYR C 252 PHE 0.013 0.001 PHE D 298 TRP 0.009 0.001 TRP A 77 HIS 0.003 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (12868) covalent geometry : angle 0.59666 / 0.30 (17659) SS BOND : bond 0.00411 / 0.19 ( 4) SS BOND : angle 0.85573 / 0.49 ( 8) hydrogen bonds : bond 0.03565 / 2.48 ( 580) hydrogen bonds : angle 4.40819 / 3.09 ( 1650) link_NAG-ASN : bond 0.00086 / 0.05 ( 5) link_NAG-ASN : angle 1.30357 / 0.78 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 0.478 Fit side-chains REVERT: A 21 ILE cc_start: 0.9283 (tp) cc_final: 0.8912 (tt) REVERT: A 264 LEU cc_start: 0.8237 (tt) cc_final: 0.8023 (tt) REVERT: A 271 MET cc_start: 0.8163 (tmm) cc_final: 0.7932 (tmm) REVERT: A 291 MET cc_start: 0.8050 (tpp) cc_final: 0.7769 (tpp) REVERT: B 21 ILE cc_start: 0.9248 (tp) cc_final: 0.8926 (tt) REVERT: B 69 GLU cc_start: 0.7578 (tt0) cc_final: 0.7263 (tt0) REVERT: B 100 ILE cc_start: 0.9071 (mt) cc_final: 0.8777 (tp) REVERT: B 138 CYS cc_start: 0.7806 (p) cc_final: 0.7384 (m) REVERT: B 271 MET cc_start: 0.7974 (tmm) cc_final: 0.7726 (tmm) REVERT: C 21 ILE cc_start: 0.9285 (tp) cc_final: 0.8931 (tt) REVERT: C 100 ILE cc_start: 0.9027 (mt) cc_final: 0.8736 (tp) REVERT: C 271 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7745 (tmm) REVERT: D 21 ILE cc_start: 0.9343 (tp) cc_final: 0.9033 (tt) REVERT: D 104 ASN cc_start: 0.7859 (OUTLIER) cc_final: 0.7656 (p0) REVERT: D 151 MET cc_start: 0.8074 (ptp) cc_final: 0.7872 (ptm) REVERT: E 17 LEU cc_start: 0.8713 (tp) cc_final: 0.8340 (tp) REVERT: E 21 ILE cc_start: 0.9342 (tp) cc_final: 0.8945 (tt) REVERT: E 100 ILE cc_start: 0.9094 (mt) cc_final: 0.8793 (tp) REVERT: E 127 MET cc_start: 0.8463 (mtt) cc_final: 0.8054 (mtt) REVERT: E 271 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7659 (tmm) REVERT: E 291 MET cc_start: 0.8856 (tpp) cc_final: 0.8647 (tpp) outliers start: 59 outliers final: 39 residues processed: 265 average time/residue: 0.0694 time to fit residues: 30.2162 Evaluate side-chains 258 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 271 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 96 optimal weight: 0.0270 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 0.0030 chunk 34 optimal weight: 0.0470 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 overall best weight: 0.1546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.142304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.113235 restraints weight = 22166.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116885 restraints weight = 14146.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119493 restraints weight = 10508.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.121327 restraints weight = 8545.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122555 restraints weight = 7377.277| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12877 Z= 0.109 Angle : 0.595 9.069 17682 Z= 0.297 Chirality : 0.044 0.175 2175 Planarity : 0.003 0.023 2121 Dihedral : 3.851 17.188 1773 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.65 % Allowed : 23.45 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.21), residues: 1610 helix: 1.18 (0.21), residues: 545 sheet: -0.54 (0.28), residues: 380 loop : -1.91 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 249 TYR 0.018 0.001 TYR A 112 PHE 0.012 0.001 PHE A 234 TRP 0.015 0.001 TRP B 77 HIS 0.004 0.001 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (12868) covalent geometry : angle 0.59529 / 0.30 (17659) SS BOND : bond 0.00216 / 0.11 ( 4) SS BOND : angle 0.59983 / 0.35 ( 8) hydrogen bonds : bond 0.03419 / 2.37 ( 580) hydrogen bonds : angle 4.26063 / 3.00 ( 1650) link_NAG-ASN : bond 0.00335 / 0.18 ( 5) link_NAG-ASN : angle 0.52420 / 0.32 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 232 time to evaluate : 0.411 Fit side-chains REVERT: A 21 ILE cc_start: 0.9231 (tp) cc_final: 0.8892 (tt) REVERT: A 127 MET cc_start: 0.8663 (mtp) cc_final: 0.8448 (mtp) REVERT: A 271 MET cc_start: 0.8134 (tmm) cc_final: 0.7884 (tmm) REVERT: B 21 ILE cc_start: 0.9167 (tp) cc_final: 0.8856 (tt) REVERT: B 138 CYS cc_start: 0.7866 (p) cc_final: 0.7443 (m) REVERT: B 270 ARG cc_start: 0.8624 (tpp80) cc_final: 0.8389 (tpp80) REVERT: B 271 MET cc_start: 0.7959 (tmm) cc_final: 0.7697 (tmm) REVERT: C 21 ILE cc_start: 0.9223 (tp) cc_final: 0.8911 (tt) REVERT: C 100 ILE cc_start: 0.8734 (mt) cc_final: 0.8444 (tp) REVERT: C 127 MET cc_start: 0.8238 (mtp) cc_final: 0.7606 (mtm) REVERT: C 271 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7820 (tmm) REVERT: C 289 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8039 (t80) REVERT: C 291 MET cc_start: 0.8526 (tpp) cc_final: 0.8064 (tpp) REVERT: D 13 ASP cc_start: 0.7330 (t70) cc_final: 0.7119 (t0) REVERT: D 21 ILE cc_start: 0.9296 (tp) cc_final: 0.9020 (tt) REVERT: D 127 MET cc_start: 0.8242 (mtp) cc_final: 0.7794 (mtm) REVERT: D 236 THR cc_start: 0.9167 (p) cc_final: 0.8919 (t) REVERT: D 291 MET cc_start: 0.8626 (tpp) cc_final: 0.8349 (tpp) REVERT: E 21 ILE cc_start: 0.9271 (tp) cc_final: 0.8921 (tt) REVERT: E 127 MET cc_start: 0.8248 (mtt) cc_final: 0.7890 (mtt) REVERT: E 271 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7626 (tmm) REVERT: E 291 MET cc_start: 0.8738 (tpp) cc_final: 0.8234 (tpp) outliers start: 46 outliers final: 29 residues processed: 262 average time/residue: 0.0734 time to fit residues: 31.1956 Evaluate side-chains 248 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 266 MET Chi-restraints excluded: chain E residue 271 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 102 optimal weight: 0.0970 chunk 94 optimal weight: 0.2980 chunk 98 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.140840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.111209 restraints weight = 22403.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114790 restraints weight = 14250.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117359 restraints weight = 10594.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119180 restraints weight = 8625.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120462 restraints weight = 7464.210| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12877 Z= 0.124 Angle : 0.622 10.109 17682 Z= 0.304 Chirality : 0.044 0.167 2175 Planarity : 0.003 0.024 2121 Dihedral : 3.797 14.131 1771 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.93 % Allowed : 24.80 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.21), residues: 1610 helix: 1.27 (0.22), residues: 545 sheet: -0.59 (0.28), residues: 375 loop : -1.98 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 249 TYR 0.018 0.001 TYR C 252 PHE 0.012 0.001 PHE A 428 TRP 0.014 0.001 TRP B 77 HIS 0.003 0.001 HIS E 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (12868) covalent geometry : angle 0.62149 / 0.30 (17659) SS BOND : bond 0.00288 / 0.14 ( 4) SS BOND : angle 0.69792 / 0.40 ( 8) hydrogen bonds : bond 0.03392 / 2.35 ( 580) hydrogen bonds : angle 4.29679 / 3.02 ( 1650) link_NAG-ASN : bond 0.00140 / 0.07 ( 5) link_NAG-ASN : angle 1.04475 / 0.60 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.298 Fit side-chains REVERT: A 21 ILE cc_start: 0.9241 (tp) cc_final: 0.8901 (tt) REVERT: A 127 MET cc_start: 0.8650 (mtp) cc_final: 0.8371 (mtp) REVERT: B 21 ILE cc_start: 0.9178 (tp) cc_final: 0.8869 (tt) REVERT: B 138 CYS cc_start: 0.7873 (p) cc_final: 0.7438 (m) REVERT: B 270 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8380 (tpp80) REVERT: B 271 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7686 (tmm) REVERT: C 21 ILE cc_start: 0.9226 (tp) cc_final: 0.8906 (tt) REVERT: C 271 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7824 (tmm) REVERT: C 275 LEU cc_start: 0.8172 (mm) cc_final: 0.7765 (mm) REVERT: C 289 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8071 (t80) REVERT: D 21 ILE cc_start: 0.9310 (tp) cc_final: 0.9018 (tt) REVERT: D 265 MET cc_start: 0.8450 (ttm) cc_final: 0.8150 (ttt) REVERT: D 291 MET cc_start: 0.8666 (tpp) cc_final: 0.8412 (tpp) REVERT: E 21 ILE cc_start: 0.9248 (tp) cc_final: 0.8886 (tt) REVERT: E 127 MET cc_start: 0.8422 (mtt) cc_final: 0.8018 (mtt) REVERT: E 271 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7669 (tmm) outliers start: 37 outliers final: 24 residues processed: 241 average time/residue: 0.0714 time to fit residues: 28.2126 Evaluate side-chains 243 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 266 MET Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 271 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 51 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 0.0970 chunk 4 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.140052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.110325 restraints weight = 22376.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113813 restraints weight = 14220.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116452 restraints weight = 10592.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118268 restraints weight = 8641.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119346 restraints weight = 7480.322| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12877 Z= 0.132 Angle : 0.629 9.836 17682 Z= 0.307 Chirality : 0.044 0.269 2175 Planarity : 0.003 0.023 2121 Dihedral : 3.810 14.234 1771 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.14 % Allowed : 25.59 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.21), residues: 1610 helix: 1.32 (0.22), residues: 545 sheet: -0.70 (0.28), residues: 375 loop : -1.97 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 249 TYR 0.020 0.001 TYR C 252 PHE 0.011 0.001 PHE A 234 TRP 0.015 0.001 TRP B 77 HIS 0.002 0.001 HIS E 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (12868) covalent geometry : angle 0.62852 / 0.31 (17659) SS BOND : bond 0.00331 / 0.16 ( 4) SS BOND : angle 0.72339 / 0.41 ( 8) hydrogen bonds : bond 0.03428 / 2.37 ( 580) hydrogen bonds : angle 4.32413 / 3.05 ( 1650) link_NAG-ASN : bond 0.00150 / 0.08 ( 5) link_NAG-ASN : angle 1.09744 / 0.65 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.313 Fit side-chains REVERT: A 21 ILE cc_start: 0.9244 (tp) cc_final: 0.8905 (tt) REVERT: A 127 MET cc_start: 0.8645 (mtp) cc_final: 0.8355 (mtp) REVERT: B 21 ILE cc_start: 0.9176 (tp) cc_final: 0.8869 (tt) REVERT: B 138 CYS cc_start: 0.7852 (p) cc_final: 0.7428 (m) REVERT: B 270 ARG cc_start: 0.8626 (tpp80) cc_final: 0.8414 (tpp80) REVERT: B 271 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7704 (tmm) REVERT: C 21 ILE cc_start: 0.9229 (tp) cc_final: 0.8909 (tt) REVERT: C 100 ILE cc_start: 0.8884 (mt) cc_final: 0.8581 (tp) REVERT: C 275 LEU cc_start: 0.8179 (mm) cc_final: 0.7760 (mm) REVERT: C 289 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8103 (t80) REVERT: C 291 MET cc_start: 0.8513 (tpt) cc_final: 0.8037 (tpp) REVERT: D 21 ILE cc_start: 0.9313 (tp) cc_final: 0.9014 (tt) REVERT: D 291 MET cc_start: 0.8755 (tpp) cc_final: 0.8493 (tpp) REVERT: E 21 ILE cc_start: 0.9234 (tp) cc_final: 0.8878 (tt) REVERT: E 127 MET cc_start: 0.8421 (mtt) cc_final: 0.8019 (mtt) REVERT: E 271 MET cc_start: 0.8006 (tmm) cc_final: 0.7788 (tmm) REVERT: E 291 MET cc_start: 0.8636 (tpp) cc_final: 0.8380 (tpp) outliers start: 27 outliers final: 23 residues processed: 241 average time/residue: 0.0734 time to fit residues: 29.0587 Evaluate side-chains 238 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 417 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 42 optimal weight: 0.0470 chunk 4 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 119 optimal weight: 0.0670 chunk 3 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111409 restraints weight = 22430.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.114929 restraints weight = 14446.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117447 restraints weight = 10810.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119231 restraints weight = 8842.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120388 restraints weight = 7673.850| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12877 Z= 0.122 Angle : 0.626 9.649 17682 Z= 0.305 Chirality : 0.045 0.285 2175 Planarity : 0.003 0.023 2121 Dihedral : 3.799 13.892 1771 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.38 % Allowed : 25.12 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.21), residues: 1610 helix: 1.31 (0.22), residues: 545 sheet: -0.71 (0.28), residues: 375 loop : -1.93 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 249 TYR 0.018 0.001 TYR C 252 PHE 0.022 0.001 PHE B 137 TRP 0.013 0.001 TRP B 77 HIS 0.002 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (12868) covalent geometry : angle 0.62565 / 0.30 (17659) SS BOND : bond 0.00300 / 0.14 ( 4) SS BOND : angle 0.69006 / 0.39 ( 8) hydrogen bonds : bond 0.03375 / 2.34 ( 580) hydrogen bonds : angle 4.30170 / 3.04 ( 1650) link_NAG-ASN : bond 0.00199 / 0.11 ( 5) link_NAG-ASN : angle 0.95638 / 0.57 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1951.20 seconds wall clock time: 34 minutes 25.27 seconds (2065.27 seconds total)