Starting phenix.real_space_refine on Sat Aug 23 14:09:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bxb_16314/08_2025/8bxb_16314.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bxb_16314/08_2025/8bxb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bxb_16314/08_2025/8bxb_16314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bxb_16314/08_2025/8bxb_16314.map" model { file = "/net/cci-nas-00/data/ceres_data/8bxb_16314/08_2025/8bxb_16314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bxb_16314/08_2025/8bxb_16314.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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: 2.78, per 1000 atoms: 0.22 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: 0.75 Conformation dependent library (CDL) restraints added in 559.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.44 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: 1.65 Time building geometry restraints manager: 1.10 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: 6503 11.98 - 23.95: 643 23.95 - 35.93: 219 35.93 - 47.90: 112 47.90 - 59.88: 47 Dihedral angle restraints: 7524 sinusoidal: 2679 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 7521 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: 5.340 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.710 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 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 : 13.499 59.880 4382 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 aren 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 covalent geometry : bond 0.00407 (12868) covalent geometry : angle 0.77856 (17659) SS BOND : bond 0.46123 ( 4) SS BOND : angle 26.70697 ( 8) hydrogen bonds : bond 0.15526 ( 580) hydrogen bonds : angle 6.18963 ( 1650) link_NAG-ASN : bond 0.00266 ( 5) link_NAG-ASN : angle 0.28934 ( 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 : 0.462 Fit side-chains REVERT: A 104 ASN cc_start: 0.7295 (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: 0.8269 (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: 0.8105 (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: 0.0673 time to fit residues: 38.6437 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 : 0.305 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.141503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.112411 restraints weight = 22627.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.116106 restraints weight = 14429.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118551 restraints weight = 10699.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120532 restraints weight = 8765.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121814 restraints weight = 7551.973| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12877 Z= 0.136 Angle : 0.554 5.711 17682 Z= 0.284 Chirality : 0.043 0.146 2175 Planarity : 0.004 0.029 2121 Dihedral : 5.247 56.532 1900 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.60 % Allowed : 19.10 % Favored : 76.31 % 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 aren not related in a simple way. whole: -1.53 (0.21), residues: 1610 helix: 0.01 (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 A 194 TYR 0.018 0.001 TYR E 121 PHE 0.018 0.001 PHE D 298 TRP 0.010 0.001 TRP B 70 HIS 0.004 0.001 HIS E 58 Details of bonding type rmsd covalent geometry : bond 0.00306 (12868) covalent geometry : angle 0.55131 (17659) SS BOND : bond 0.00182 ( 4) SS BOND : angle 2.10483 ( 8) hydrogen bonds : bond 0.04010 ( 580) hydrogen bonds : angle 4.53322 ( 1650) link_NAG-ASN : bond 0.00193 ( 5) link_NAG-ASN : angle 1.38589 ( 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 305 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 247 time to evaluate : 0.335 Fit side-chains REVERT: A 104 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7920 (p0) REVERT: A 265 MET cc_start: 0.8607 (ttp) cc_final: 0.8319 (ttt) REVERT: A 271 MET cc_start: 0.7738 (tmm) cc_final: 0.7364 (tmm) REVERT: A 275 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8098 (mt) REVERT: B 100 ILE cc_start: 0.8997 (mt) cc_final: 0.8597 (tp) REVERT: B 265 MET cc_start: 0.8473 (ttp) cc_final: 0.8232 (ttp) REVERT: B 271 MET cc_start: 0.7511 (tmm) cc_final: 0.7164 (tmm) REVERT: B 275 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8071 (mt) REVERT: C 21 ILE cc_start: 0.9236 (tp) cc_final: 0.8824 (tt) REVERT: C 87 LYS cc_start: 0.8753 (mtpt) cc_final: 0.8524 (mtpt) REVERT: C 127 MET cc_start: 0.8368 (mtp) cc_final: 0.8070 (mtp) REVERT: C 196 GLN cc_start: 0.7995 (mp10) cc_final: 0.7759 (mp10) REVERT: C 271 MET cc_start: 0.7862 (tmm) cc_final: 0.7458 (tmm) REVERT: C 275 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8087 (mt) REVERT: D 21 ILE cc_start: 0.9300 (tp) cc_final: 0.8922 (tt) REVERT: D 23 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7851 (t-170) REVERT: D 104 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7799 (p0) REVERT: D 196 GLN cc_start: 0.8020 (mp10) cc_final: 0.7777 (mp10) REVERT: D 275 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8162 (mt) REVERT: D 291 MET cc_start: 0.8712 (tpp) cc_final: 0.8386 (tpp) REVERT: E 17 LEU cc_start: 0.8743 (tp) cc_final: 0.8471 (tp) REVERT: E 21 ILE cc_start: 0.9267 (tp) cc_final: 0.8882 (tt) REVERT: E 23 HIS cc_start: 0.8018 (OUTLIER) cc_final: 0.7817 (t-170) REVERT: E 239 MET cc_start: 0.8088 (ttp) cc_final: 0.7726 (ttt) REVERT: E 265 MET cc_start: 0.8369 (ttp) cc_final: 0.8058 (ttp) REVERT: E 271 MET cc_start: 0.7581 (tmm) cc_final: 0.7361 (tmm) REVERT: E 275 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8023 (mt) REVERT: E 287 TYR cc_start: 0.8057 (t80) cc_final: 0.7599 (t80) outliers start: 58 outliers final: 32 residues processed: 278 average time/residue: 0.0677 time to fit residues: 30.4194 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 : 0.305 ------------------------------------------------------------------------------- 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: 0.2980 chunk 99 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 130 optimal weight: 0.0370 chunk 101 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 54 optimal weight: 0.0370 chunk 126 optimal weight: 3.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.144234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116281 restraints weight = 21718.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120107 restraints weight = 13588.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122787 restraints weight = 9840.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124739 restraints weight = 7845.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126050 restraints weight = 6660.322| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12877 Z= 0.100 Angle : 0.532 8.476 17682 Z= 0.267 Chirality : 0.043 0.154 2175 Planarity : 0.003 0.026 2121 Dihedral : 4.092 18.687 1880 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.04 % Allowed : 20.05 % Favored : 75.91 % 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 aren not related in a simple way. whole: -1.02 (0.21), residues: 1610 helix: 0.60 (0.21), residues: 545 sheet: -0.60 (0.28), residues: 400 loop : -1.79 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 249 TYR 0.020 0.001 TYR C 287 PHE 0.012 0.001 PHE C 428 TRP 0.009 0.001 TRP E 185 HIS 0.004 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00220 (12868) covalent geometry : angle 0.53072 (17659) SS BOND : bond 0.00312 ( 4) SS BOND : angle 0.94364 ( 8) hydrogen bonds : bond 0.03557 ( 580) hydrogen bonds : angle 4.25556 ( 1650) link_NAG-ASN : bond 0.00295 ( 5) link_NAG-ASN : angle 1.18184 ( 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 299 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 248 time to evaluate : 0.425 Fit side-chains REVERT: A 104 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7875 (p0) REVERT: A 265 MET cc_start: 0.8536 (ttp) cc_final: 0.8259 (ttt) REVERT: A 291 MET cc_start: 0.8750 (tpp) cc_final: 0.8534 (tpp) REVERT: B 271 MET cc_start: 0.7557 (tmm) cc_final: 0.7175 (tmm) REVERT: C 21 ILE cc_start: 0.9245 (tp) cc_final: 0.8845 (tt) REVERT: C 196 GLN cc_start: 0.7978 (mp10) cc_final: 0.7689 (mp10) REVERT: C 271 MET cc_start: 0.7746 (tmm) cc_final: 0.7370 (tmm) REVERT: C 291 MET cc_start: 0.8471 (tpt) cc_final: 0.8191 (tpp) REVERT: D 21 ILE cc_start: 0.9313 (tp) cc_final: 0.8941 (tt) REVERT: D 23 HIS cc_start: 0.8025 (OUTLIER) cc_final: 0.7739 (t-170) REVERT: D 104 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7698 (p0) REVERT: D 127 MET cc_start: 0.8158 (mtp) cc_final: 0.7921 (mtp) REVERT: D 196 GLN cc_start: 0.8001 (mp10) cc_final: 0.7719 (mp10) REVERT: E 17 LEU cc_start: 0.8752 (tp) cc_final: 0.8478 (tp) REVERT: E 21 ILE cc_start: 0.9283 (tp) cc_final: 0.8899 (tt) REVERT: E 265 MET cc_start: 0.8362 (ttp) cc_final: 0.8081 (ttp) REVERT: E 271 MET cc_start: 0.7555 (tmm) cc_final: 0.7327 (tmm) REVERT: E 287 TYR cc_start: 0.8106 (t80) cc_final: 0.7721 (t80) outliers start: 51 outliers final: 27 residues processed: 275 average time/residue: 0.0727 time to fit residues: 32.1276 Evaluate side-chains 255 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU 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 273 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 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 245 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 104 ASN Chi-restraints excluded: chain D residue 163 VAL 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 74 GLN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 96 optimal weight: 0.7980 chunk 147 optimal weight: 0.0070 chunk 150 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 144 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.141724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111992 restraints weight = 22635.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115745 restraints weight = 14340.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118425 restraints weight = 10585.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120334 restraints weight = 8580.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121411 restraints weight = 7391.217| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1782 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= 0.114 Angle : 0.532 7.371 17682 Z= 0.270 Chirality : 0.043 0.170 2175 Planarity : 0.003 0.026 2121 Dihedral : 4.016 18.114 1880 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.99 % Allowed : 20.21 % Favored : 74.80 % 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 aren not related in a simple way. whole: -0.81 (0.21), residues: 1610 helix: 0.93 (0.22), residues: 545 sheet: -0.53 (0.28), residues: 400 loop : -1.79 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 249 TYR 0.017 0.001 TYR C 287 PHE 0.010 0.001 PHE D 298 TRP 0.008 0.001 TRP E 185 HIS 0.005 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00262 (12868) covalent geometry : angle 0.53106 (17659) SS BOND : bond 0.00321 ( 4) SS BOND : angle 0.76139 ( 8) hydrogen bonds : bond 0.03468 ( 580) hydrogen bonds : angle 4.20748 ( 1650) link_NAG-ASN : bond 0.00215 ( 5) link_NAG-ASN : angle 1.23402 ( 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 299 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 236 time to evaluate : 0.488 Fit side-chains REVERT: A 104 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7870 (p0) REVERT: A 271 MET cc_start: 0.7743 (tmm) cc_final: 0.7399 (tmm) REVERT: A 429 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7838 (mt) REVERT: B 21 ILE cc_start: 0.9280 (tp) cc_final: 0.8879 (tt) REVERT: B 100 ILE cc_start: 0.8944 (mt) cc_final: 0.8614 (tp) REVERT: B 271 MET cc_start: 0.7603 (tmm) cc_final: 0.7232 (tmm) REVERT: C 21 ILE cc_start: 0.9252 (tp) cc_final: 0.8852 (tt) REVERT: C 196 GLN cc_start: 0.8054 (mp10) cc_final: 0.7783 (mp10) REVERT: C 271 MET cc_start: 0.7759 (tmm) cc_final: 0.7402 (tmm) REVERT: D 21 ILE cc_start: 0.9322 (tp) cc_final: 0.8952 (tt) REVERT: D 23 HIS cc_start: 0.8122 (OUTLIER) cc_final: 0.7803 (t-170) REVERT: D 104 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7692 (p0) REVERT: D 196 GLN cc_start: 0.8083 (mp10) cc_final: 0.7788 (mp10) REVERT: E 17 LEU cc_start: 0.8751 (tp) cc_final: 0.8463 (tp) REVERT: E 21 ILE cc_start: 0.9288 (tp) cc_final: 0.8913 (tt) REVERT: E 265 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8113 (ttt) REVERT: E 271 MET cc_start: 0.7557 (tmm) cc_final: 0.7172 (tmm) outliers start: 63 outliers final: 36 residues processed: 280 average time/residue: 0.0672 time to fit residues: 30.4314 Evaluate side-chains 265 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 424 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 245 LEU 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 245 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 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 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 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 265 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 130 optimal weight: 0.6980 chunk 90 optimal weight: 0.3980 chunk 139 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.144215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.115718 restraints weight = 22144.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119241 restraints weight = 14360.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.121776 restraints weight = 10741.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.123386 restraints weight = 8769.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.124682 restraints weight = 7642.110| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1991 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= 0.121 Angle : 0.540 8.317 17682 Z= 0.272 Chirality : 0.044 0.174 2175 Planarity : 0.003 0.024 2121 Dihedral : 3.975 17.299 1880 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.83 % Allowed : 21.24 % Favored : 73.93 % 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 aren not related in a simple way. whole: -0.72 (0.21), residues: 1610 helix: 1.09 (0.22), residues: 545 sheet: -0.46 (0.28), residues: 400 loop : -1.83 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 249 TYR 0.014 0.001 TYR C 252 PHE 0.011 0.001 PHE D 298 TRP 0.010 0.001 TRP C 77 HIS 0.002 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00285 (12868) covalent geometry : angle 0.53884 (17659) SS BOND : bond 0.00363 ( 4) SS BOND : angle 0.82545 ( 8) hydrogen bonds : bond 0.03430 ( 580) hydrogen bonds : angle 4.20990 ( 1650) link_NAG-ASN : bond 0.00205 ( 5) link_NAG-ASN : angle 1.23061 ( 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 297 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 236 time to evaluate : 0.585 Fit side-chains REVERT: A 271 MET cc_start: 0.7951 (tmm) cc_final: 0.7670 (tmm) REVERT: A 291 MET cc_start: 0.8748 (tpp) cc_final: 0.8543 (tpp) REVERT: B 21 ILE cc_start: 0.9312 (tp) cc_final: 0.8928 (tt) REVERT: B 127 MET cc_start: 0.8699 (mtp) cc_final: 0.8332 (mtm) REVERT: B 138 CYS cc_start: 0.7580 (p) cc_final: 0.7317 (m) REVERT: B 271 MET cc_start: 0.7690 (tmm) cc_final: 0.7371 (tmm) REVERT: C 21 ILE cc_start: 0.9283 (tp) cc_final: 0.8907 (tt) REVERT: C 100 ILE cc_start: 0.8914 (mt) cc_final: 0.8651 (tp) REVERT: C 196 GLN cc_start: 0.8073 (mp10) cc_final: 0.7842 (mp10) REVERT: C 271 MET cc_start: 0.7832 (tmm) cc_final: 0.7563 (tmm) REVERT: D 21 ILE cc_start: 0.9320 (tp) cc_final: 0.8971 (tt) REVERT: D 23 HIS cc_start: 0.7980 (OUTLIER) cc_final: 0.7714 (t-170) REVERT: D 104 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7581 (p0) REVERT: D 127 MET cc_start: 0.8263 (mtp) cc_final: 0.8040 (mtp) REVERT: D 196 GLN cc_start: 0.8101 (mp10) cc_final: 0.7858 (mp10) REVERT: D 291 MET cc_start: 0.8657 (tpp) cc_final: 0.8360 (tpp) REVERT: E 17 LEU cc_start: 0.8673 (tp) cc_final: 0.8345 (tp) REVERT: E 21 ILE cc_start: 0.9306 (tp) cc_final: 0.8909 (tt) REVERT: E 265 MET cc_start: 0.8506 (ttp) cc_final: 0.8302 (ttp) REVERT: E 271 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7410 (tmm) outliers start: 61 outliers final: 41 residues processed: 279 average time/residue: 0.0847 time to fit residues: 38.7268 Evaluate side-chains 267 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 289 PHE Chi-restraints excluded: chain A residue 424 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 B residue 245 LEU Chi-restraints excluded: chain B residue 275 LEU 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 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 188 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 LEU 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 62 THR 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 256 LEU 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: 0.8980 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: 2.9990 chunk 16 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 119 optimal weight: 0.0000 chunk 79 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3761 r_free = 0.3761 target = 0.142190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113863 restraints weight = 22185.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.117097 restraints weight = 14385.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.119362 restraints weight = 10813.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.121193 restraints weight = 8923.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.122354 restraints weight = 7755.296| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12877 Z= 0.146 Angle : 0.566 7.316 17682 Z= 0.286 Chirality : 0.044 0.172 2175 Planarity : 0.003 0.023 2121 Dihedral : 4.034 17.129 1878 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.99 % Allowed : 21.39 % Favored : 73.61 % 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 aren not related in a simple way. whole: -0.73 (0.21), residues: 1610 helix: 1.13 (0.22), residues: 545 sheet: -0.49 (0.28), residues: 400 loop : -1.86 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 249 TYR 0.018 0.001 TYR C 252 PHE 0.011 0.001 PHE D 298 TRP 0.010 0.001 TRP A 159 HIS 0.003 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00343 (12868) covalent geometry : angle 0.56433 (17659) SS BOND : bond 0.00398 ( 4) SS BOND : angle 0.97285 ( 8) hydrogen bonds : bond 0.03470 ( 580) hydrogen bonds : angle 4.33071 ( 1650) link_NAG-ASN : bond 0.00181 ( 5) link_NAG-ASN : angle 1.43542 ( 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 292 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 229 time to evaluate : 0.515 Fit side-chains REVERT: A 21 ILE cc_start: 0.9285 (tp) cc_final: 0.8903 (tt) REVERT: A 271 MET cc_start: 0.8052 (tmm) cc_final: 0.7782 (tmm) REVERT: A 291 MET cc_start: 0.8782 (tpp) cc_final: 0.8527 (tpp) REVERT: A 429 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7864 (mt) REVERT: B 21 ILE cc_start: 0.9336 (tp) cc_final: 0.9050 (tt) REVERT: B 69 GLU cc_start: 0.7569 (tt0) cc_final: 0.7331 (tt0) REVERT: B 138 CYS cc_start: 0.7629 (p) cc_final: 0.7384 (m) REVERT: B 271 MET cc_start: 0.7832 (tmm) cc_final: 0.7514 (tmm) REVERT: C 21 ILE cc_start: 0.9262 (tp) cc_final: 0.8898 (tt) REVERT: C 100 ILE cc_start: 0.8996 (mt) cc_final: 0.8721 (tp) REVERT: C 196 GLN cc_start: 0.8115 (mp10) cc_final: 0.7915 (mp10) REVERT: C 271 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7658 (tmm) REVERT: D 21 ILE cc_start: 0.9330 (tp) cc_final: 0.8987 (tt) REVERT: D 104 ASN cc_start: 0.7920 (OUTLIER) cc_final: 0.7550 (p0) REVERT: D 196 GLN cc_start: 0.8094 (mp10) cc_final: 0.7860 (mp10) REVERT: D 291 MET cc_start: 0.8707 (tpp) cc_final: 0.8395 (tpp) REVERT: E 21 ILE cc_start: 0.9327 (tp) cc_final: 0.8925 (tt) REVERT: E 227 MET cc_start: 0.7852 (tmm) cc_final: 0.7196 (tpt) REVERT: E 271 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7514 (tmm) outliers start: 63 outliers final: 42 residues processed: 272 average time/residue: 0.0823 time to fit residues: 36.9849 Evaluate side-chains 265 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 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 B residue 245 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 275 LEU 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 271 MET 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 256 LEU 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 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 268 SER Chi-restraints excluded: chain E residue 271 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 78 optimal weight: 2.9990 chunk 154 optimal weight: 0.3980 chunk 97 optimal weight: 0.0570 chunk 139 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.0170 chunk 71 optimal weight: 0.6980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3785 r_free = 0.3785 target = 0.144098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115555 restraints weight = 22045.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.119099 restraints weight = 14286.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.121403 restraints weight = 10680.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123296 restraints weight = 8785.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.124530 restraints weight = 7600.381| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2341 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= 0.112 Angle : 0.566 11.196 17682 Z= 0.282 Chirality : 0.044 0.168 2175 Planarity : 0.003 0.022 2121 Dihedral : 3.913 17.269 1878 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.52 % Allowed : 22.50 % Favored : 72.98 % 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 aren not related in a simple way. whole: -0.69 (0.21), residues: 1610 helix: 1.17 (0.22), residues: 545 sheet: -0.24 (0.29), residues: 365 loop : -1.95 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 249 TYR 0.016 0.001 TYR C 252 PHE 0.010 0.001 PHE D 298 TRP 0.009 0.001 TRP A 77 HIS 0.002 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00262 (12868) covalent geometry : angle 0.56536 (17659) SS BOND : bond 0.00313 ( 4) SS BOND : angle 0.70543 ( 8) hydrogen bonds : bond 0.03386 ( 580) hydrogen bonds : angle 4.28845 ( 1650) link_NAG-ASN : bond 0.00263 ( 5) link_NAG-ASN : angle 1.11136 ( 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 289 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.444 Fit side-chains REVERT: A 21 ILE cc_start: 0.9260 (tp) cc_final: 0.8917 (tt) REVERT: A 271 MET cc_start: 0.8057 (tmm) cc_final: 0.7802 (tmm) REVERT: A 291 MET cc_start: 0.8818 (tpp) cc_final: 0.8440 (tpp) REVERT: B 21 ILE cc_start: 0.9295 (tp) cc_final: 0.9016 (tt) REVERT: B 100 ILE cc_start: 0.8912 (mt) cc_final: 0.8652 (tp) REVERT: B 270 ARG cc_start: 0.8621 (tpp80) cc_final: 0.8374 (tpp80) REVERT: B 271 MET cc_start: 0.7914 (tmm) cc_final: 0.7652 (tmm) REVERT: B 287 TYR cc_start: 0.8273 (t80) cc_final: 0.8028 (t80) REVERT: C 21 ILE cc_start: 0.9254 (tp) cc_final: 0.8917 (tt) REVERT: C 271 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7751 (tmm) REVERT: C 275 LEU cc_start: 0.8101 (mm) cc_final: 0.7762 (mm) REVERT: D 21 ILE cc_start: 0.9312 (tp) cc_final: 0.9005 (tt) REVERT: D 127 MET cc_start: 0.8346 (mtp) cc_final: 0.8091 (mtp) REVERT: D 196 GLN cc_start: 0.8067 (mp10) cc_final: 0.7835 (mp10) REVERT: D 291 MET cc_start: 0.8685 (tpp) cc_final: 0.8341 (tpp) REVERT: E 21 ILE cc_start: 0.9312 (tp) cc_final: 0.8929 (tt) REVERT: E 227 MET cc_start: 0.7830 (tmm) cc_final: 0.7188 (tpt) REVERT: E 271 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7547 (tmm) REVERT: E 291 MET cc_start: 0.8786 (tpp) cc_final: 0.8293 (tpp) outliers start: 57 outliers final: 38 residues processed: 268 average time/residue: 0.0786 time to fit residues: 34.4320 Evaluate side-chains 256 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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 424 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 B residue 245 LEU 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 163 VAL 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 C residue 424 LEU Chi-restraints excluded: chain D residue 62 THR 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 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 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 271 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 96 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 121 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3807 r_free = 0.3807 target = 0.145370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116789 restraints weight = 21589.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.120230 restraints weight = 14221.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122715 restraints weight = 10738.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124303 restraints weight = 8799.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125689 restraints weight = 7681.127| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12877 Z= 0.125 Angle : 0.603 10.527 17682 Z= 0.296 Chirality : 0.044 0.161 2175 Planarity : 0.003 0.022 2121 Dihedral : 3.858 13.147 1876 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.12 % Allowed : 22.19 % Favored : 73.69 % 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 aren not related in a simple way. whole: -0.72 (0.21), residues: 1610 helix: 1.22 (0.22), residues: 545 sheet: -0.37 (0.29), residues: 365 loop : -1.94 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 249 TYR 0.020 0.001 TYR A 112 PHE 0.013 0.001 PHE D 103 TRP 0.011 0.001 TRP C 77 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00299 (12868) covalent geometry : angle 0.60251 (17659) SS BOND : bond 0.00321 ( 4) SS BOND : angle 0.77561 ( 8) hydrogen bonds : bond 0.03360 ( 580) hydrogen bonds : angle 4.37259 ( 1650) link_NAG-ASN : bond 0.00203 ( 5) link_NAG-ASN : angle 1.22181 ( 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 270 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 218 time to evaluate : 0.320 Fit side-chains REVERT: A 21 ILE cc_start: 0.9270 (tp) cc_final: 0.8905 (tt) REVERT: A 271 MET cc_start: 0.8109 (tmm) cc_final: 0.7878 (tmm) REVERT: A 291 MET cc_start: 0.8787 (tpp) cc_final: 0.8492 (tpp) REVERT: B 21 ILE cc_start: 0.9244 (tp) cc_final: 0.8949 (tt) REVERT: B 271 MET cc_start: 0.7948 (tmm) cc_final: 0.7723 (tmm) REVERT: B 287 TYR cc_start: 0.8281 (t80) cc_final: 0.7991 (t80) REVERT: C 21 ILE cc_start: 0.9255 (tp) cc_final: 0.8922 (tt) REVERT: C 275 LEU cc_start: 0.8130 (mm) cc_final: 0.7783 (mm) REVERT: C 289 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8192 (t80) REVERT: D 21 ILE cc_start: 0.9312 (tp) cc_final: 0.9005 (tt) REVERT: D 127 MET cc_start: 0.8390 (mtp) cc_final: 0.8165 (mtp) REVERT: D 291 MET cc_start: 0.8723 (tpp) cc_final: 0.8356 (tpp) REVERT: E 21 ILE cc_start: 0.9311 (tp) cc_final: 0.8935 (tt) REVERT: E 227 MET cc_start: 0.7864 (tmm) cc_final: 0.7292 (tpt) REVERT: E 271 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7683 (tmm) outliers start: 52 outliers final: 38 residues processed: 253 average time/residue: 0.0752 time to fit residues: 31.0103 Evaluate side-chains 251 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 424 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 B residue 245 LEU 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 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 417 THR Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 62 THR 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 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 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 268 SER 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: 0.9980 chunk 63 optimal weight: 0.7980 chunk 102 optimal weight: 0.0370 chunk 94 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 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 = 0.3797 r_free = 0.3797 target = 0.144728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115874 restraints weight = 21797.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119293 restraints weight = 14380.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.121764 restraints weight = 10876.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123457 restraints weight = 8948.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.124572 restraints weight = 7797.007| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12877 Z= 0.134 Angle : 0.623 9.944 17682 Z= 0.303 Chirality : 0.044 0.162 2175 Planarity : 0.003 0.022 2121 Dihedral : 3.897 13.130 1876 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.57 % Allowed : 23.61 % Favored : 72.82 % 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 aren not related in a simple way. whole: -0.76 (0.21), residues: 1610 helix: 1.20 (0.22), residues: 545 sheet: -0.46 (0.28), residues: 365 loop : -1.95 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 249 TYR 0.019 0.001 TYR C 252 PHE 0.010 0.001 PHE A 425 TRP 0.017 0.001 TRP B 77 HIS 0.002 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00323 (12868) covalent geometry : angle 0.62169 (17659) SS BOND : bond 0.00344 ( 4) SS BOND : angle 0.78996 ( 8) hydrogen bonds : bond 0.03394 ( 580) hydrogen bonds : angle 4.42359 ( 1650) link_NAG-ASN : bond 0.00194 ( 5) link_NAG-ASN : angle 1.30975 ( 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 268 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 0.462 Fit side-chains REVERT: A 21 ILE cc_start: 0.9267 (tp) cc_final: 0.8920 (tt) REVERT: A 271 MET cc_start: 0.8164 (tmm) cc_final: 0.7960 (tmm) REVERT: A 291 MET cc_start: 0.8781 (tpp) cc_final: 0.8462 (tpp) REVERT: B 21 ILE cc_start: 0.9240 (tp) cc_final: 0.8943 (tt) REVERT: B 271 MET cc_start: 0.7938 (tmm) cc_final: 0.7704 (tmm) REVERT: C 21 ILE cc_start: 0.9257 (tp) cc_final: 0.8925 (tt) REVERT: C 289 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8188 (t80) REVERT: D 21 ILE cc_start: 0.9330 (tp) cc_final: 0.9022 (tt) REVERT: D 127 MET cc_start: 0.8422 (mtp) cc_final: 0.8179 (mtp) REVERT: D 291 MET cc_start: 0.8741 (tpp) cc_final: 0.8441 (tpp) REVERT: E 21 ILE cc_start: 0.9313 (tp) cc_final: 0.8940 (tt) REVERT: E 227 MET cc_start: 0.7870 (tmm) cc_final: 0.7300 (tpt) REVERT: E 271 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7744 (tmm) outliers start: 45 outliers final: 37 residues processed: 254 average time/residue: 0.0825 time to fit residues: 34.0507 Evaluate side-chains 255 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 417 THR Chi-restraints excluded: chain A residue 424 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 B residue 254 ILE Chi-restraints excluded: chain B residue 295 ASN 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 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 62 THR 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 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 271 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 64 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 0.4980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3812 r_free = 0.3812 target = 0.145580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116112 restraints weight = 22069.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119547 restraints weight = 14786.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122044 restraints weight = 11290.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123589 restraints weight = 9335.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.124943 restraints weight = 8217.642| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12877 Z= 0.123 Angle : 0.635 13.395 17682 Z= 0.307 Chirality : 0.044 0.232 2175 Planarity : 0.003 0.024 2121 Dihedral : 3.815 14.301 1876 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.93 % Allowed : 24.56 % 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 aren not related in a simple way. whole: -0.75 (0.21), residues: 1610 helix: 1.28 (0.22), residues: 545 sheet: -0.60 (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 C 249 TYR 0.019 0.001 TYR C 252 PHE 0.011 0.001 PHE A 425 TRP 0.019 0.001 TRP B 77 HIS 0.002 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00294 (12868) covalent geometry : angle 0.63393 (17659) SS BOND : bond 0.00309 ( 4) SS BOND : angle 0.70350 ( 8) hydrogen bonds : bond 0.03400 ( 580) hydrogen bonds : angle 4.37783 ( 1650) link_NAG-ASN : bond 0.00234 ( 5) link_NAG-ASN : angle 1.17063 ( 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 259 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.527 Fit side-chains REVERT: A 21 ILE cc_start: 0.9267 (tp) cc_final: 0.8925 (tt) REVERT: A 271 MET cc_start: 0.8170 (tmm) cc_final: 0.7959 (tmm) REVERT: A 291 MET cc_start: 0.8720 (tpp) cc_final: 0.8084 (tpp) REVERT: B 21 ILE cc_start: 0.9202 (tp) cc_final: 0.8912 (tt) REVERT: B 138 CYS cc_start: 0.7730 (p) cc_final: 0.7292 (m) REVERT: B 287 TYR cc_start: 0.8182 (t80) cc_final: 0.7883 (t80) REVERT: C 21 ILE cc_start: 0.9242 (tp) cc_final: 0.8924 (tt) REVERT: C 289 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8182 (t80) REVERT: D 21 ILE cc_start: 0.9318 (tp) cc_final: 0.9023 (tt) REVERT: D 127 MET cc_start: 0.8390 (mtp) cc_final: 0.8137 (mtp) REVERT: D 291 MET cc_start: 0.8767 (tpp) cc_final: 0.8471 (tpp) REVERT: E 21 ILE cc_start: 0.9295 (tp) cc_final: 0.8929 (tt) REVERT: E 227 MET cc_start: 0.7870 (tmm) cc_final: 0.7275 (tpt) REVERT: E 271 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7775 (tmm) outliers start: 37 outliers final: 31 residues processed: 249 average time/residue: 0.0844 time to fit residues: 33.9384 Evaluate side-chains 249 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 424 LEU 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 254 ILE Chi-restraints excluded: chain B residue 424 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 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 62 THR 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 275 LEU 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 271 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 42 optimal weight: 0.0570 chunk 4 optimal weight: 9.9990 chunk 153 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 146 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 119 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3818 r_free = 0.3818 target = 0.146183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117050 restraints weight = 22066.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120476 restraints weight = 14652.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122982 restraints weight = 11137.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124736 restraints weight = 9190.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125884 restraints weight = 8012.799| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12877 Z= 0.116 Angle : 0.631 11.048 17682 Z= 0.304 Chirality : 0.045 0.281 2175 Planarity : 0.003 0.023 2121 Dihedral : 3.758 14.211 1876 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.17 % Allowed : 25.12 % Favored : 71.71 % 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 aren not related in a simple way. whole: -0.64 (0.21), residues: 1610 helix: 1.36 (0.22), residues: 540 sheet: -0.61 (0.28), residues: 375 loop : -1.77 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 249 TYR 0.017 0.001 TYR C 252 PHE 0.011 0.001 PHE A 425 TRP 0.017 0.001 TRP B 77 HIS 0.002 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00276 (12868) covalent geometry : angle 0.63048 (17659) SS BOND : bond 0.00297 ( 4) SS BOND : angle 0.66933 ( 8) hydrogen bonds : bond 0.03373 ( 580) hydrogen bonds : angle 4.32978 ( 1650) link_NAG-ASN : bond 0.00251 ( 5) link_NAG-ASN : angle 1.08741 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2011.95 seconds wall clock time: 35 minutes 33.63 seconds (2133.63 seconds total)