Starting phenix.real_space_refine on Fri Aug 22 20:04:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jv6_36669/08_2025/8jv6_36669.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jv6_36669/08_2025/8jv6_36669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jv6_36669/08_2025/8jv6_36669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jv6_36669/08_2025/8jv6_36669.map" model { file = "/net/cci-nas-00/data/ceres_data/8jv6_36669/08_2025/8jv6_36669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jv6_36669/08_2025/8jv6_36669.cif" } resolution = 3.43 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= 0.160 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 Cl 3 4.86 5 C 4704 2.51 5 N 1254 2.21 5 O 1449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 7458 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2402 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 297} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2402 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 297} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2402 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 297} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'NAG': 3, 'P6E': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 98 Unusual residues: {'NAG': 5, 'P6E': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 84 Unusual residues: {'NAG': 4, 'P6E': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.78, per 1000 atoms: 0.24 Number of scatterers: 7458 At special positions: 0 Unit cell: (89.89, 86.33, 113.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 3 17.00 S 48 16.00 O 1449 8.00 N 1254 7.00 C 4704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.04 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 264 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 152 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 220 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 264 " - pdb=" SG CYS C 273 " distance=2.03 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 403 " - " ASN A 187 " " NAG B 405 " - " ASN B 187 " " NAG C 404 " - " ASN C 187 " Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 423.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 17 sheets defined 22.2% alpha, 52.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.901A pdb=" N THR A 128 " --> pdb=" O PRO A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 213 through 219 removed outlier: 4.182A pdb=" N HIS A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 334 through 358 removed outlier: 3.682A pdb=" N THR A 338 " --> pdb=" O ASN A 334 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 213 through 219 removed outlier: 4.186A pdb=" N HIS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 241 Processing helix chain 'B' and resid 245 through 250 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 334 through 358 removed outlier: 3.705A pdb=" N THR B 338 " --> pdb=" O ASN B 334 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 213 through 219 removed outlier: 4.181A pdb=" N HIS C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'C' and resid 245 through 253 removed outlier: 4.009A pdb=" N VAL C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG C 252 " --> pdb=" O ILE C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 334 through 358 removed outlier: 3.757A pdb=" N THR C 338 " --> pdb=" O ASN C 334 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 351 " --> pdb=" O ALA C 347 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 72 Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 79 removed outlier: 3.502A pdb=" N ALA A 75 " --> pdb=" O TRP A 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 147 through 153 removed outlier: 9.987A pdb=" N VAL A 147 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N TRP A 167 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR A 149 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N LEU A 165 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG A 151 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 163 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N SER A 101 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 324 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N PHE A 103 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N PHE A 322 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU A 105 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE A 320 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A 113 " --> pdb=" O ARG A 312 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ARG A 312 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N THR A 115 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N GLU A 310 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 147 through 153 removed outlier: 9.987A pdb=" N VAL A 147 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N TRP A 167 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR A 149 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N LEU A 165 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG A 151 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 163 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N SER A 101 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 324 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N PHE A 103 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N PHE A 322 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU A 105 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE A 320 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A 113 " --> pdb=" O ARG A 312 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ARG A 312 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N THR A 115 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N GLU A 310 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 62 Processing sheet with id=AA8, first strand: chain 'B' and resid 147 through 153 removed outlier: 10.017A pdb=" N VAL B 147 " --> pdb=" O TRP B 167 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N TRP B 167 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N THR B 149 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N LEU B 165 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG B 151 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 163 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N SER B 101 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL B 324 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N PHE B 103 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE B 322 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU B 105 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE B 320 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN B 113 " --> pdb=" O ARG B 312 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG B 312 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR B 115 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N GLU B 310 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 64 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 64 through 72 Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 79 removed outlier: 3.501A pdb=" N ALA B 75 " --> pdb=" O TRP B 87 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AB4, first strand: chain 'C' and resid 64 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 64 through 72 Processing sheet with id=AB6, first strand: chain 'C' and resid 75 through 79 Processing sheet with id=AB7, first strand: chain 'C' and resid 147 through 153 removed outlier: 3.804A pdb=" N VAL C 147 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU C 163 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ARG C 151 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N THR C 161 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N SER C 101 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL C 324 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE C 103 " --> pdb=" O PHE C 322 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE C 322 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU C 105 " --> pdb=" O ILE C 320 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 320 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN C 113 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG C 312 " --> pdb=" O ASN C 113 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N THR C 115 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N GLU C 310 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 147 through 153 removed outlier: 3.804A pdb=" N VAL C 147 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU C 163 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ARG C 151 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N THR C 161 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N SER C 101 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL C 324 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE C 103 " --> pdb=" O PHE C 322 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE C 322 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU C 105 " --> pdb=" O ILE C 320 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 320 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN C 113 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG C 312 " --> pdb=" O ASN C 113 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N THR C 115 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N GLU C 310 " --> pdb=" O THR C 115 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 942 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: 1.23 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1239 1.31 - 1.43: 2073 1.43 - 1.56: 4241 1.56 - 1.69: 1 1.69 - 1.82: 69 Bond restraints: 7623 Sorted by residual: bond pdb=" C02 P6E A 404 " pdb=" N10 P6E A 404 " ideal model delta sigma weight residual 1.365 1.452 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" N18 P6E C 405 " pdb=" S16 P6E C 405 " ideal model delta sigma weight residual 1.619 1.705 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" N18 P6E A 404 " pdb=" S16 P6E A 404 " ideal model delta sigma weight residual 1.619 1.705 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" N18 P6E B 406 " pdb=" S16 P6E B 406 " ideal model delta sigma weight residual 1.619 1.705 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C02 P6E C 405 " pdb=" N10 P6E C 405 " ideal model delta sigma weight residual 1.365 1.449 -0.084 2.00e-02 2.50e+03 1.78e+01 ... (remaining 7618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 10347 3.73 - 7.47: 40 7.47 - 11.20: 8 11.20 - 14.94: 0 14.94 - 18.67: 3 Bond angle restraints: 10398 Sorted by residual: angle pdb=" O17 P6E A 404 " pdb=" S16 P6E A 404 " pdb=" O19 P6E A 404 " ideal model delta sigma weight residual 119.45 100.78 18.67 3.00e+00 1.11e-01 3.87e+01 angle pdb=" O17 P6E C 405 " pdb=" S16 P6E C 405 " pdb=" O19 P6E C 405 " ideal model delta sigma weight residual 119.45 100.82 18.63 3.00e+00 1.11e-01 3.86e+01 angle pdb=" O17 P6E B 406 " pdb=" S16 P6E B 406 " pdb=" O19 P6E B 406 " ideal model delta sigma weight residual 119.45 100.86 18.59 3.00e+00 1.11e-01 3.84e+01 angle pdb=" C02 P6E B 406 " pdb=" N10 P6E B 406 " pdb=" C11 P6E B 406 " ideal model delta sigma weight residual 129.18 120.48 8.70 3.00e+00 1.11e-01 8.41e+00 angle pdb=" C02 P6E C 405 " pdb=" N10 P6E C 405 " pdb=" C11 P6E C 405 " ideal model delta sigma weight residual 129.18 120.90 8.28 3.00e+00 1.11e-01 7.61e+00 ... (remaining 10393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 4155 18.08 - 36.15: 420 36.15 - 54.23: 123 54.23 - 72.30: 21 72.30 - 90.38: 9 Dihedral angle restraints: 4728 sinusoidal: 1989 harmonic: 2739 Sorted by residual: dihedral pdb=" CB CYS C 220 " pdb=" SG CYS C 220 " pdb=" SG CYS C 230 " pdb=" CB CYS C 230 " ideal model delta sinusoidal sigma weight residual 93.00 -176.62 -90.38 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 230 " pdb=" CB CYS A 230 " ideal model delta sinusoidal sigma weight residual 93.00 -176.64 -90.36 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" CB CYS B 220 " pdb=" SG CYS B 220 " pdb=" SG CYS B 230 " pdb=" CB CYS B 230 " ideal model delta sinusoidal sigma weight residual 93.00 -176.73 -90.27 1 1.00e+01 1.00e-02 9.65e+01 ... (remaining 4725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 739 0.033 - 0.067: 266 0.067 - 0.100: 127 0.100 - 0.133: 49 0.133 - 0.167: 4 Chirality restraints: 1185 Sorted by residual: chirality pdb=" CB ILE C 173 " pdb=" CA ILE C 173 " pdb=" CG1 ILE C 173 " pdb=" CG2 ILE C 173 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA ILE A 320 " pdb=" N ILE A 320 " pdb=" C ILE A 320 " pdb=" CB ILE A 320 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA ILE B 74 " pdb=" N ILE B 74 " pdb=" C ILE B 74 " pdb=" CB ILE B 74 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 1182 not shown) Planarity restraints: 1353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 122 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO C 123 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 123 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 123 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 209 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO A 210 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 210 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 210 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 286 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 287 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " 0.021 5.00e-02 4.00e+02 ... (remaining 1350 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 360 2.73 - 3.27: 7062 3.27 - 3.81: 11532 3.81 - 4.36: 13509 4.36 - 4.90: 24539 Nonbonded interactions: 57002 Sorted by model distance: nonbonded pdb=" OH TYR A 302 " pdb=" OD1 ASP C 91 " model vdw 2.184 3.040 nonbonded pdb=" OD1 ASP A 91 " pdb=" OH TYR B 302 " model vdw 2.186 3.040 nonbonded pdb=" OD1 ASP B 91 " pdb=" OH TYR C 302 " model vdw 2.199 3.040 nonbonded pdb=" O ASP C 145 " pdb=" OG SER C 166 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR A 130 " pdb=" OD2 ASP A 134 " model vdw 2.288 3.040 ... (remaining 56997 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 43 through 403) selection = (chain 'B' and resid 43 through 403) selection = (chain 'C' and resid 43 through 403) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.470 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.005 0.087 7641 Z= 0.230 Angle : 0.757 18.670 10437 Z= 0.347 Chirality : 0.045 0.167 1185 Planarity : 0.005 0.075 1350 Dihedral : 15.508 89.183 2925 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 16.08 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.26 (0.27), residues: 942 helix: 0.61 (0.40), residues: 198 sheet: 0.76 (0.27), residues: 318 loop : -0.41 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 148 TYR 0.016 0.001 TYR A 53 PHE 0.011 0.001 PHE A 299 TRP 0.010 0.001 TRP A 167 HIS 0.001 0.000 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 7623) covalent geometry : angle 0.75134 (10398) SS BOND : bond 0.00361 ( 15) SS BOND : angle 1.88311 ( 30) hydrogen bonds : bond 0.13302 ( 302) hydrogen bonds : angle 5.36628 ( 942) link_NAG-ASN : bond 0.00010 ( 3) link_NAG-ASN : angle 0.93770 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.192 Fit side-chains REVERT: C 267 ASP cc_start: 0.7166 (m-30) cc_final: 0.6606 (m-30) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0791 time to fit residues: 7.8103 Evaluate side-chains 72 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.0040 chunk 5 optimal weight: 0.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.165730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.119920 restraints weight = 7528.901| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.23 r_work: 0.3017 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7641 Z= 0.111 Angle : 0.530 6.404 10437 Z= 0.269 Chirality : 0.044 0.156 1185 Planarity : 0.004 0.054 1350 Dihedral : 8.872 58.785 1323 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.61 % Allowed : 16.47 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.27), residues: 942 helix: 1.32 (0.42), residues: 180 sheet: 0.92 (0.27), residues: 318 loop : -0.08 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 148 TYR 0.014 0.001 TYR C 318 PHE 0.009 0.001 PHE A 297 TRP 0.010 0.001 TRP C 167 HIS 0.001 0.000 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7623) covalent geometry : angle 0.52284 (10398) SS BOND : bond 0.00445 ( 15) SS BOND : angle 1.67031 ( 30) hydrogen bonds : bond 0.02938 ( 302) hydrogen bonds : angle 4.28603 ( 942) link_NAG-ASN : bond 0.00213 ( 3) link_NAG-ASN : angle 0.90021 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.259 Fit side-chains REVERT: A 172 LYS cc_start: 0.8222 (tppt) cc_final: 0.7817 (mttp) REVERT: A 259 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8427 (pt0) REVERT: A 285 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7893 (mttp) REVERT: A 320 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8545 (mm) REVERT: B 320 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8810 (mm) REVERT: B 346 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7354 (mp) REVERT: C 118 LYS cc_start: 0.7705 (mtmt) cc_final: 0.7444 (mtpt) REVERT: C 320 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8627 (mm) outliers start: 20 outliers final: 6 residues processed: 89 average time/residue: 0.0810 time to fit residues: 9.8764 Evaluate side-chains 81 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 320 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.0770 chunk 73 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.156980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.111488 restraints weight = 7563.848| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.20 r_work: 0.2910 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 7641 Z= 0.234 Angle : 0.653 9.801 10437 Z= 0.333 Chirality : 0.048 0.172 1185 Planarity : 0.004 0.044 1350 Dihedral : 8.589 57.905 1323 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.27 % Allowed : 18.95 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.20 (0.27), residues: 942 helix: 0.67 (0.40), residues: 198 sheet: 0.84 (0.27), residues: 300 loop : -0.57 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 280 TYR 0.016 0.002 TYR C 318 PHE 0.013 0.002 PHE B 102 TRP 0.012 0.002 TRP C 262 HIS 0.002 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 7623) covalent geometry : angle 0.63933 (10398) SS BOND : bond 0.00505 ( 15) SS BOND : angle 2.45763 ( 30) hydrogen bonds : bond 0.03469 ( 302) hydrogen bonds : angle 4.47971 ( 942) link_NAG-ASN : bond 0.00162 ( 3) link_NAG-ASN : angle 1.44423 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.250 Fit side-chains REVERT: A 172 LYS cc_start: 0.8318 (tppt) cc_final: 0.7953 (mttp) REVERT: A 259 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8387 (pt0) REVERT: B 118 LYS cc_start: 0.7831 (mtmt) cc_final: 0.7355 (mmtp) REVERT: B 249 MET cc_start: 0.7820 (ttm) cc_final: 0.7589 (ttm) REVERT: B 320 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8777 (mm) REVERT: C 108 MET cc_start: 0.8868 (ppp) cc_final: 0.8375 (ptt) REVERT: C 320 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8695 (mm) REVERT: C 346 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7169 (mp) outliers start: 25 outliers final: 11 residues processed: 97 average time/residue: 0.0700 time to fit residues: 9.1116 Evaluate side-chains 84 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 346 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.162073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.116389 restraints weight = 7625.120| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.16 r_work: 0.2933 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7641 Z= 0.127 Angle : 0.546 7.665 10437 Z= 0.278 Chirality : 0.044 0.139 1185 Planarity : 0.004 0.038 1350 Dihedral : 7.691 53.634 1323 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.66 % Allowed : 19.22 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.37 (0.27), residues: 942 helix: 0.93 (0.41), residues: 198 sheet: 0.69 (0.27), residues: 324 loop : -0.36 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 206 TYR 0.013 0.001 TYR C 318 PHE 0.010 0.001 PHE A 297 TRP 0.011 0.001 TRP C 167 HIS 0.001 0.000 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7623) covalent geometry : angle 0.53837 (10398) SS BOND : bond 0.00483 ( 15) SS BOND : angle 1.72458 ( 30) hydrogen bonds : bond 0.02757 ( 302) hydrogen bonds : angle 4.10280 ( 942) link_NAG-ASN : bond 0.00053 ( 3) link_NAG-ASN : angle 1.20348 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.193 Fit side-chains REVERT: A 172 LYS cc_start: 0.8285 (tppt) cc_final: 0.7955 (mttp) REVERT: A 259 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8377 (pt0) REVERT: B 118 LYS cc_start: 0.7816 (mtmt) cc_final: 0.7308 (mmtp) REVERT: B 320 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8797 (mm) REVERT: C 108 MET cc_start: 0.8878 (ppp) cc_final: 0.8330 (ptt) REVERT: C 320 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8640 (mm) REVERT: C 346 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7220 (mp) outliers start: 28 outliers final: 12 residues processed: 93 average time/residue: 0.0772 time to fit residues: 9.5733 Evaluate side-chains 84 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 346 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 71 optimal weight: 0.0040 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 72 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 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 = 0.3705 r_free = 0.3705 target = 0.159389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.114018 restraints weight = 7585.274| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.10 r_work: 0.2932 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7641 Z= 0.143 Angle : 0.561 6.315 10437 Z= 0.284 Chirality : 0.044 0.141 1185 Planarity : 0.004 0.033 1350 Dihedral : 7.144 46.160 1323 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.92 % Allowed : 18.56 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.33 (0.27), residues: 942 helix: 1.00 (0.41), residues: 198 sheet: 0.66 (0.27), residues: 324 loop : -0.44 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.014 0.001 TYR C 318 PHE 0.011 0.001 PHE B 297 TRP 0.007 0.001 TRP A 262 HIS 0.001 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 7623) covalent geometry : angle 0.55290 (10398) SS BOND : bond 0.00410 ( 15) SS BOND : angle 1.68349 ( 30) hydrogen bonds : bond 0.02826 ( 302) hydrogen bonds : angle 4.09282 ( 942) link_NAG-ASN : bond 0.00038 ( 3) link_NAG-ASN : angle 1.37790 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.252 Fit side-chains REVERT: A 172 LYS cc_start: 0.8272 (tppt) cc_final: 0.7965 (mttp) REVERT: A 259 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8393 (pt0) REVERT: B 118 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7417 (mmtp) REVERT: C 66 SER cc_start: 0.8194 (OUTLIER) cc_final: 0.7949 (p) REVERT: C 108 MET cc_start: 0.8892 (ppp) cc_final: 0.8342 (ptt) REVERT: C 320 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8651 (mm) outliers start: 30 outliers final: 15 residues processed: 93 average time/residue: 0.0663 time to fit residues: 8.3893 Evaluate side-chains 88 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 320 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 66 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.160155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.115289 restraints weight = 7551.476| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.06 r_work: 0.2934 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7641 Z= 0.141 Angle : 0.566 6.577 10437 Z= 0.286 Chirality : 0.044 0.142 1185 Planarity : 0.004 0.031 1350 Dihedral : 6.993 43.825 1323 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.18 % Allowed : 18.69 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.35 (0.27), residues: 942 helix: 1.02 (0.41), residues: 198 sheet: 0.68 (0.27), residues: 324 loop : -0.45 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.014 0.001 TYR C 318 PHE 0.010 0.001 PHE A 299 TRP 0.019 0.001 TRP A 167 HIS 0.001 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7623) covalent geometry : angle 0.55604 (10398) SS BOND : bond 0.00371 ( 15) SS BOND : angle 1.94201 ( 30) hydrogen bonds : bond 0.02794 ( 302) hydrogen bonds : angle 4.10207 ( 942) link_NAG-ASN : bond 0.00011 ( 3) link_NAG-ASN : angle 1.38666 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.256 Fit side-chains REVERT: A 172 LYS cc_start: 0.8265 (tppt) cc_final: 0.7993 (mttp) REVERT: A 259 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8383 (pt0) REVERT: B 118 LYS cc_start: 0.7800 (mtmt) cc_final: 0.7304 (mmtp) REVERT: C 66 SER cc_start: 0.8147 (OUTLIER) cc_final: 0.7916 (p) REVERT: C 108 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8542 (ptp) REVERT: C 172 LYS cc_start: 0.8330 (tppt) cc_final: 0.7687 (mttt) REVERT: C 320 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8643 (mm) outliers start: 32 outliers final: 18 residues processed: 94 average time/residue: 0.0702 time to fit residues: 8.9811 Evaluate side-chains 88 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 320 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 0.0070 chunk 6 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.174531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119111 restraints weight = 7596.916| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.80 r_work: 0.3026 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 7641 Z= 0.219 Angle : 0.637 7.470 10437 Z= 0.325 Chirality : 0.047 0.162 1185 Planarity : 0.004 0.036 1350 Dihedral : 7.229 42.134 1323 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.18 % Allowed : 18.95 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.12 (0.27), residues: 942 helix: 0.87 (0.40), residues: 198 sheet: 0.66 (0.27), residues: 303 loop : -0.65 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 280 TYR 0.016 0.002 TYR C 318 PHE 0.013 0.002 PHE C 299 TRP 0.010 0.002 TRP C 87 HIS 0.001 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 7623) covalent geometry : angle 0.62413 (10398) SS BOND : bond 0.00459 ( 15) SS BOND : angle 2.29784 ( 30) hydrogen bonds : bond 0.03229 ( 302) hydrogen bonds : angle 4.30120 ( 942) link_NAG-ASN : bond 0.00165 ( 3) link_NAG-ASN : angle 1.72079 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.258 Fit side-chains REVERT: A 172 LYS cc_start: 0.8328 (tppt) cc_final: 0.8050 (mttp) REVERT: A 256 MET cc_start: 0.8419 (mmm) cc_final: 0.8206 (tpp) REVERT: A 259 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8398 (pt0) REVERT: C 108 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8563 (ptp) REVERT: C 172 LYS cc_start: 0.8370 (tppt) cc_final: 0.7752 (mttt) REVERT: C 320 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8722 (mm) outliers start: 32 outliers final: 22 residues processed: 95 average time/residue: 0.0747 time to fit residues: 9.6230 Evaluate side-chains 93 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 320 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 41 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 73 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.159251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.113328 restraints weight = 7639.978| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.23 r_work: 0.2925 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7641 Z= 0.126 Angle : 0.560 6.248 10437 Z= 0.284 Chirality : 0.044 0.139 1185 Planarity : 0.004 0.037 1350 Dihedral : 6.944 43.423 1323 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.40 % Allowed : 19.74 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.33 (0.27), residues: 942 helix: 1.13 (0.42), residues: 198 sheet: 0.65 (0.27), residues: 324 loop : -0.51 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 276 TYR 0.013 0.001 TYR C 318 PHE 0.011 0.001 PHE B 297 TRP 0.015 0.002 TRP A 167 HIS 0.001 0.000 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7623) covalent geometry : angle 0.55154 (10398) SS BOND : bond 0.00304 ( 15) SS BOND : angle 1.76526 ( 30) hydrogen bonds : bond 0.02710 ( 302) hydrogen bonds : angle 4.06185 ( 942) link_NAG-ASN : bond 0.00040 ( 3) link_NAG-ASN : angle 1.32651 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.180 Fit side-chains REVERT: A 172 LYS cc_start: 0.8318 (tppt) cc_final: 0.7992 (mttp) REVERT: A 256 MET cc_start: 0.8459 (mmm) cc_final: 0.8200 (tpp) REVERT: A 259 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8395 (pt0) REVERT: B 118 LYS cc_start: 0.7944 (mtpt) cc_final: 0.7329 (mmtp) REVERT: B 172 LYS cc_start: 0.8362 (mttp) cc_final: 0.7909 (mtpt) REVERT: C 108 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8517 (ptp) REVERT: C 172 LYS cc_start: 0.8333 (tppt) cc_final: 0.7699 (mttt) REVERT: C 320 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8640 (mm) outliers start: 26 outliers final: 18 residues processed: 87 average time/residue: 0.0768 time to fit residues: 9.0719 Evaluate side-chains 88 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 320 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 38 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.171653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.117550 restraints weight = 7621.252| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.77 r_work: 0.3038 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 7641 Z= 0.256 Angle : 0.656 7.448 10437 Z= 0.336 Chirality : 0.048 0.167 1185 Planarity : 0.005 0.044 1350 Dihedral : 7.284 41.751 1323 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.44 % Allowed : 19.35 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.02 (0.27), residues: 942 helix: 0.89 (0.41), residues: 198 sheet: 0.50 (0.26), residues: 315 loop : -0.79 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 280 TYR 0.016 0.002 TYR C 318 PHE 0.013 0.002 PHE A 299 TRP 0.011 0.002 TRP C 87 HIS 0.001 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00643 ( 7623) covalent geometry : angle 0.64395 (10398) SS BOND : bond 0.00482 ( 15) SS BOND : angle 2.26377 ( 30) hydrogen bonds : bond 0.03378 ( 302) hydrogen bonds : angle 4.30469 ( 942) link_NAG-ASN : bond 0.00167 ( 3) link_NAG-ASN : angle 1.68979 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 68 time to evaluate : 0.189 Fit side-chains REVERT: A 172 LYS cc_start: 0.8286 (tppt) cc_final: 0.7972 (mttp) REVERT: A 256 MET cc_start: 0.8440 (mmm) cc_final: 0.8227 (tpp) REVERT: A 259 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8398 (pt0) REVERT: B 118 LYS cc_start: 0.7934 (mtpt) cc_final: 0.7313 (mmtp) REVERT: B 172 LYS cc_start: 0.8408 (mttp) cc_final: 0.7952 (mtpt) REVERT: C 108 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8597 (ptp) REVERT: C 172 LYS cc_start: 0.8393 (tppt) cc_final: 0.7777 (mttt) REVERT: C 320 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8724 (mm) outliers start: 34 outliers final: 26 residues processed: 96 average time/residue: 0.0702 time to fit residues: 9.0298 Evaluate side-chains 97 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 320 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.175406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120005 restraints weight = 7534.915| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.74 r_work: 0.2995 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7641 Z= 0.154 Angle : 0.583 6.532 10437 Z= 0.296 Chirality : 0.045 0.149 1185 Planarity : 0.004 0.045 1350 Dihedral : 7.129 42.298 1323 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.92 % Allowed : 19.61 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.13 (0.27), residues: 942 helix: 1.06 (0.42), residues: 198 sheet: 0.57 (0.27), residues: 306 loop : -0.67 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.014 0.001 TYR C 318 PHE 0.012 0.001 PHE A 299 TRP 0.012 0.001 TRP A 167 HIS 0.001 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 7623) covalent geometry : angle 0.57371 (10398) SS BOND : bond 0.00350 ( 15) SS BOND : angle 1.91767 ( 30) hydrogen bonds : bond 0.02896 ( 302) hydrogen bonds : angle 4.14259 ( 942) link_NAG-ASN : bond 0.00046 ( 3) link_NAG-ASN : angle 1.44284 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.240 Fit side-chains REVERT: A 172 LYS cc_start: 0.8298 (tppt) cc_final: 0.8004 (mttp) REVERT: A 256 MET cc_start: 0.8390 (mmm) cc_final: 0.8104 (tpp) REVERT: A 259 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8401 (pt0) REVERT: B 118 LYS cc_start: 0.7978 (mtpt) cc_final: 0.7389 (mmtp) REVERT: B 172 LYS cc_start: 0.8430 (mttp) cc_final: 0.7974 (mtpt) REVERT: C 108 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8530 (ptp) REVERT: C 172 LYS cc_start: 0.8389 (tppt) cc_final: 0.7777 (mttt) REVERT: C 320 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8686 (mm) outliers start: 30 outliers final: 24 residues processed: 94 average time/residue: 0.0693 time to fit residues: 8.8107 Evaluate side-chains 99 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 320 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 0.0070 chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.159191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.114579 restraints weight = 7520.819| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.02 r_work: 0.2945 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7641 Z= 0.110 Angle : 0.545 6.504 10437 Z= 0.276 Chirality : 0.043 0.136 1185 Planarity : 0.004 0.043 1350 Dihedral : 6.863 43.204 1323 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.53 % Allowed : 20.13 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.34 (0.27), residues: 942 helix: 1.20 (0.42), residues: 198 sheet: 0.67 (0.27), residues: 324 loop : -0.55 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 85 TYR 0.013 0.001 TYR C 318 PHE 0.010 0.001 PHE B 297 TRP 0.015 0.001 TRP A 167 HIS 0.001 0.000 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7623) covalent geometry : angle 0.53690 (10398) SS BOND : bond 0.00302 ( 15) SS BOND : angle 1.68035 ( 30) hydrogen bonds : bond 0.02556 ( 302) hydrogen bonds : angle 3.97950 ( 942) link_NAG-ASN : bond 0.00087 ( 3) link_NAG-ASN : angle 1.20298 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1464.27 seconds wall clock time: 25 minutes 43.57 seconds (1543.57 seconds total)