Starting phenix.real_space_refine on Thu Jul 2 07:22:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jv6_36669/07_2026/8jv6_36669.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jv6_36669/07_2026/8jv6_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8jv6_36669/07_2026/8jv6_36669.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jv6_36669/07_2026/8jv6_36669.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jv6_36669/07_2026/8jv6_36669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jv6_36669/07_2026/8jv6_36669.map" model { file = "/net/cci-nas-00/data/ceres_data/8jv6_36669/07_2026/8jv6_36669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jv6_36669/07_2026/8jv6_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 chiralities: 4 Time building chain proxies: 1.53, per 1000 atoms: 0.21 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: 0.44 Conformation dependent library (CDL) restraints added in 300.3 milliseconds 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: 0.23 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: 1.15 Time building geometry restraints manager: 0.63 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: 3947 18.08 - 36.15: 406 36.15 - 54.23: 102 54.23 - 72.30: 12 72.30 - 90.38: 9 Dihedral angle restraints: 4476 sinusoidal: 1737 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 4473 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: 1.160 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.360 Find NCS groups from input model: 0.160 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 : 15.254 89.183 2673 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 are 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/Z covalent geometry : bond 0.00488 / 0.23 ( 7623) covalent geometry : angle 0.75134 / 0.34 (10398) SS BOND : bond 0.00361 / 0.26 ( 15) SS BOND : angle 1.88311 / 1.41 ( 30) hydrogen bonds : bond 0.13302 / 8.52 ( 302) hydrogen bonds : angle 5.36628 / 3.75 ( 942) link_NAG-ASN : bond 0.00010 / 0.01 ( 3) link_NAG-ASN : angle 0.93770 / 0.53 ( 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 : 0.199 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: 0.0728 time to fit residues: 7.3070 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 : 0.261 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.174222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113731 restraints weight = 7476.982| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.92 r_work: 0.3071 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7641 Z= 0.110 Angle : 0.529 6.194 10437 Z= 0.268 Chirality : 0.044 0.143 1185 Planarity : 0.004 0.054 1350 Dihedral : 5.889 45.716 1071 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.48 % Allowed : 16.47 % Favored : 81.05 % 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 are not related in a simple way. whole: 0.75 (0.27), residues: 942 helix: 1.32 (0.42), residues: 180 sheet: 0.91 (0.27), residues: 318 loop : -0.08 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 148 TYR 0.013 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/Z covalent geometry : bond 0.00258 / 0.11 ( 7623) covalent geometry : angle 0.52218 / 0.27 (10398) SS BOND : bond 0.00442 / 0.32 ( 15) SS BOND : angle 1.66732 / 1.24 ( 30) hydrogen bonds : bond 0.02944 / 1.92 ( 302) hydrogen bonds : angle 4.29132 / 2.96 ( 942) link_NAG-ASN : bond 0.00209 / 0.10 ( 3) link_NAG-ASN : angle 0.77272 / 0.45 ( 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 94 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.276 Fit side-chains REVERT: A 172 LYS cc_start: 0.8148 (tppt) cc_final: 0.7766 (mttp) REVERT: A 259 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8299 (pt0) REVERT: A 285 LYS cc_start: 0.8336 (mttt) cc_final: 0.7827 (mttp) REVERT: A 320 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8475 (mm) REVERT: B 320 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8836 (mm) REVERT: B 346 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.7036 (mp) REVERT: C 118 LYS cc_start: 0.7507 (mtmt) cc_final: 0.7242 (mtpt) REVERT: C 320 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8613 (mm) outliers start: 19 outliers final: 5 residues processed: 89 average time/residue: 0.0772 time to fit residues: 9.4398 Evaluate side-chains 80 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 73 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 50.0000 chunk 49 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3693 r_free = 0.3693 target = 0.158196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113263 restraints weight = 7535.094| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.11 r_work: 0.2929 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7641 Z= 0.195 Angle : 0.618 10.263 10437 Z= 0.314 Chirality : 0.046 0.168 1185 Planarity : 0.004 0.043 1350 Dihedral : 6.180 43.657 1071 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.40 % Allowed : 18.69 % Favored : 77.91 % 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 are not related in a simple way. whole: 0.30 (0.27), residues: 942 helix: 0.79 (0.41), residues: 198 sheet: 0.90 (0.27), residues: 300 loop : -0.53 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 280 TYR 0.015 0.002 TYR C 318 PHE 0.013 0.002 PHE C 102 TRP 0.013 0.002 TRP C 167 HIS 0.001 0.001 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.19 ( 7623) covalent geometry : angle 0.60696 / 0.31 (10398) SS BOND : bond 0.00465 / 0.32 ( 15) SS BOND : angle 2.11886 / 1.56 ( 30) hydrogen bonds : bond 0.03275 / 2.13 ( 302) hydrogen bonds : angle 4.35449 / 3.00 ( 942) link_NAG-ASN : bond 0.00132 / 0.06 ( 3) link_NAG-ASN : angle 1.29789 / 0.74 ( 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 104 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.168 Fit side-chains REVERT: A 172 LYS cc_start: 0.8342 (tppt) cc_final: 0.7983 (mttp) REVERT: A 259 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8447 (pt0) REVERT: B 118 LYS cc_start: 0.7809 (mtmt) cc_final: 0.7347 (mmtp) REVERT: B 320 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8782 (mm) REVERT: C 108 MET cc_start: 0.8815 (ppp) cc_final: 0.8328 (ptt) REVERT: C 320 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8666 (mm) REVERT: C 346 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7314 (mp) outliers start: 26 outliers final: 12 residues processed: 100 average time/residue: 0.0722 time to fit residues: 9.8618 Evaluate side-chains 86 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 chunk 55 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN ** B 140 ASN ** 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 = 0.3739 r_free = 0.3739 target = 0.162392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117421 restraints weight = 7666.441| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.08 r_work: 0.2971 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7641 Z= 0.118 Angle : 0.538 7.626 10437 Z= 0.272 Chirality : 0.043 0.137 1185 Planarity : 0.004 0.038 1350 Dihedral : 6.021 44.254 1071 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.01 % Allowed : 20.26 % Favored : 76.73 % 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 are not related in a simple way. whole: 0.44 (0.27), residues: 942 helix: 0.96 (0.41), residues: 198 sheet: 0.76 (0.27), residues: 324 loop : -0.33 (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/Z covalent geometry : bond 0.00286 / 0.12 ( 7623) covalent geometry : angle 0.53047 / 0.27 (10398) SS BOND : bond 0.00333 / 0.22 ( 15) SS BOND : angle 1.65051 / 1.24 ( 30) hydrogen bonds : bond 0.02687 / 1.77 ( 302) hydrogen bonds : angle 4.03452 / 2.77 ( 942) link_NAG-ASN : bond 0.00048 / 0.02 ( 3) link_NAG-ASN : angle 0.93226 / 0.53 ( 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 99 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.180 Fit side-chains REVERT: A 172 LYS cc_start: 0.8283 (tppt) cc_final: 0.7900 (mttp) REVERT: A 259 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8394 (pt0) REVERT: B 118 LYS cc_start: 0.7844 (mtmt) cc_final: 0.7379 (mmtp) REVERT: B 172 LYS cc_start: 0.8325 (ttmm) cc_final: 0.7769 (mtpt) REVERT: B 320 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8783 (mm) REVERT: C 108 MET cc_start: 0.8844 (ppp) cc_final: 0.8298 (ptt) REVERT: C 118 LYS cc_start: 0.7803 (mtmt) cc_final: 0.7529 (mtpt) REVERT: C 320 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8626 (mm) REVERT: C 346 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7184 (mp) outliers start: 23 outliers final: 8 residues processed: 92 average time/residue: 0.0866 time to fit residues: 10.6414 Evaluate side-chains 84 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 248 ILE 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 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: 2.9990 chunk 40 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 60 optimal weight: 0.0470 chunk 80 optimal weight: 0.0170 chunk 29 optimal weight: 0.0670 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN B 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.164170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.116654 restraints weight = 7565.875| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.20 r_work: 0.2993 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7641 Z= 0.095 Angle : 0.510 6.388 10437 Z= 0.259 Chirality : 0.043 0.140 1185 Planarity : 0.003 0.034 1350 Dihedral : 5.791 44.634 1071 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.14 % Allowed : 19.87 % Favored : 76.99 % 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 are not related in a simple way. whole: 0.63 (0.27), residues: 942 helix: 1.30 (0.44), residues: 180 sheet: 1.03 (0.27), residues: 318 loop : -0.37 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.012 0.001 TYR C 318 PHE 0.009 0.001 PHE B 297 TRP 0.009 0.001 TRP A 167 HIS 0.001 0.000 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.09 ( 7623) covalent geometry : angle 0.50513 / 0.26 (10398) SS BOND : bond 0.00369 / 0.27 ( 15) SS BOND : angle 1.38959 / 1.03 ( 30) hydrogen bonds : bond 0.02472 / 1.63 ( 302) hydrogen bonds : angle 3.91475 / 2.69 ( 942) link_NAG-ASN : bond 0.00144 / 0.07 ( 3) link_NAG-ASN : angle 0.80172 / 0.45 ( 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 93 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.271 Fit side-chains REVERT: A 172 LYS cc_start: 0.8274 (tppt) cc_final: 0.7953 (mttp) REVERT: B 346 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7349 (mp) REVERT: C 108 MET cc_start: 0.8787 (ppp) cc_final: 0.8258 (ptt) REVERT: C 118 LYS cc_start: 0.7813 (mtmt) cc_final: 0.7420 (mtpt) REVERT: C 320 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8604 (mm) outliers start: 24 outliers final: 9 residues processed: 90 average time/residue: 0.0916 time to fit residues: 11.1242 Evaluate side-chains 77 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 63 VAL 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: 1.9990 chunk 85 optimal weight: 3.9990 chunk 86 optimal weight: 0.0040 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.162292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.115983 restraints weight = 7569.859| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.19 r_work: 0.2937 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7641 Z= 0.134 Angle : 0.559 6.969 10437 Z= 0.282 Chirality : 0.044 0.142 1185 Planarity : 0.004 0.031 1350 Dihedral : 5.868 43.731 1071 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.14 % Allowed : 19.35 % 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 are not related in a simple way. whole: 0.46 (0.27), residues: 942 helix: 1.03 (0.41), residues: 198 sheet: 0.72 (0.27), residues: 339 loop : -0.35 (0.30), residues: 405 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 297 TRP 0.017 0.001 TRP A 167 HIS 0.001 0.001 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.13 ( 7623) covalent geometry : angle 0.54912 / 0.28 (10398) SS BOND : bond 0.00349 / 0.26 ( 15) SS BOND : angle 1.92384 / 1.32 ( 30) hydrogen bonds : bond 0.02721 / 1.77 ( 302) hydrogen bonds : angle 3.99035 / 2.76 ( 942) link_NAG-ASN : bond 0.00013 / 0.01 ( 3) link_NAG-ASN : angle 1.04942 / 0.60 ( 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 99 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.276 Fit side-chains REVERT: A 172 LYS cc_start: 0.8283 (tppt) cc_final: 0.7986 (mttp) REVERT: A 256 MET cc_start: 0.8416 (mmm) cc_final: 0.8180 (tpp) REVERT: B 118 LYS cc_start: 0.7773 (mtpt) cc_final: 0.7230 (mmtp) REVERT: B 320 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8771 (mm) REVERT: C 108 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8315 (ptt) REVERT: C 172 LYS cc_start: 0.8191 (tppt) cc_final: 0.7496 (mttt) REVERT: C 320 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8646 (mm) outliers start: 24 outliers final: 14 residues processed: 94 average time/residue: 0.0943 time to fit residues: 11.8705 Evaluate side-chains 87 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 129 CYS 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 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 182 LEU 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 B residue 320 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 108 MET 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: 0.7980 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 9 optimal weight: 0.0070 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 86 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 116 GLN ** 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 = 0.3741 r_free = 0.3741 target = 0.162694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.117912 restraints weight = 7541.569| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.05 r_work: 0.2981 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7641 Z= 0.111 Angle : 0.537 7.372 10437 Z= 0.269 Chirality : 0.043 0.133 1185 Planarity : 0.003 0.030 1350 Dihedral : 5.818 44.284 1071 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.01 % Allowed : 19.35 % Favored : 77.65 % 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 are not related in a simple way. whole: 0.62 (0.27), residues: 942 helix: 1.29 (0.43), residues: 180 sheet: 0.91 (0.27), residues: 333 loop : -0.31 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 148 TYR 0.013 0.001 TYR C 318 PHE 0.009 0.001 PHE B 297 TRP 0.013 0.001 TRP A 167 HIS 0.001 0.000 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 7623) covalent geometry : angle 0.52971 / 0.27 (10398) SS BOND : bond 0.00317 / 0.24 ( 15) SS BOND : angle 1.65938 / 1.16 ( 30) hydrogen bonds : bond 0.02547 / 1.67 ( 302) hydrogen bonds : angle 3.92728 / 2.72 ( 942) link_NAG-ASN : bond 0.00078 / 0.04 ( 3) link_NAG-ASN : angle 0.92850 / 0.52 ( 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 89 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.271 Fit side-chains REVERT: A 172 LYS cc_start: 0.8292 (tppt) cc_final: 0.7984 (mttp) REVERT: B 118 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7214 (mmtp) REVERT: B 320 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8766 (mm) REVERT: C 108 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8264 (ptt) REVERT: C 172 LYS cc_start: 0.8224 (tppt) cc_final: 0.7549 (mttt) REVERT: C 320 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8621 (mm) outliers start: 23 outliers final: 16 residues processed: 83 average time/residue: 0.0971 time to fit residues: 10.8357 Evaluate side-chains 83 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 129 CYS 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 291 VAL Chi-restraints excluded: chain B residue 63 VAL 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 B residue 320 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 108 MET 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: 6.9990 chunk 59 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 88 optimal weight: 0.0070 chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3716 r_free = 0.3716 target = 0.160285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.114775 restraints weight = 7658.172| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.20 r_work: 0.2941 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7641 Z= 0.156 Angle : 0.578 7.486 10437 Z= 0.291 Chirality : 0.044 0.147 1185 Planarity : 0.004 0.029 1350 Dihedral : 5.996 43.484 1071 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.88 % Allowed : 19.61 % 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 are not related in a simple way. whole: 0.54 (0.27), residues: 942 helix: 1.07 (0.41), residues: 198 sheet: 0.89 (0.27), residues: 321 loop : -0.34 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.015 0.001 TYR C 318 PHE 0.011 0.001 PHE A 299 TRP 0.009 0.001 TRP A 167 HIS 0.001 0.000 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 7623) covalent geometry : angle 0.56866 / 0.29 (10398) SS BOND : bond 0.00388 / 0.30 ( 15) SS BOND : angle 1.91182 / 1.37 ( 30) hydrogen bonds : bond 0.02827 / 1.83 ( 302) hydrogen bonds : angle 4.01679 / 2.77 ( 942) link_NAG-ASN : bond 0.00078 / 0.04 ( 3) link_NAG-ASN : angle 1.23813 / 0.70 ( 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 92 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.277 Fit side-chains REVERT: A 172 LYS cc_start: 0.8313 (tppt) cc_final: 0.8027 (mttp) REVERT: A 256 MET cc_start: 0.8464 (mmm) cc_final: 0.8215 (tpp) REVERT: B 118 LYS cc_start: 0.7766 (mtpt) cc_final: 0.7158 (mmtp) REVERT: B 320 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8735 (mm) REVERT: C 108 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8535 (ptp) REVERT: C 172 LYS cc_start: 0.8325 (tppt) cc_final: 0.7670 (mttt) REVERT: C 285 LYS cc_start: 0.8132 (mttt) cc_final: 0.7731 (mttp) REVERT: C 289 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.7974 (t0) REVERT: C 320 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8645 (mm) outliers start: 22 outliers final: 17 residues processed: 87 average time/residue: 0.1006 time to fit residues: 11.7424 Evaluate side-chains 86 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 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 291 VAL Chi-restraints excluded: chain B residue 63 VAL 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 B residue 320 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 289 ASN 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: 3.9990 chunk 59 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 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: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.158052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.112007 restraints weight = 7628.019| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.23 r_work: 0.2882 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 7641 Z= 0.211 Angle : 0.639 8.319 10437 Z= 0.323 Chirality : 0.046 0.161 1185 Planarity : 0.004 0.031 1350 Dihedral : 6.396 42.070 1071 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.66 % Allowed : 18.82 % 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 are not related in a simple way. whole: 0.22 (0.27), residues: 942 helix: 0.91 (0.41), residues: 198 sheet: 0.64 (0.27), residues: 309 loop : -0.53 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 280 TYR 0.016 0.001 TYR C 318 PHE 0.012 0.002 PHE C 299 TRP 0.012 0.002 TRP A 87 HIS 0.001 0.001 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.21 ( 7623) covalent geometry : angle 0.62789 / 0.32 (10398) SS BOND : bond 0.00450 / 0.34 ( 15) SS BOND : angle 2.20858 / 1.59 ( 30) hydrogen bonds : bond 0.03200 / 2.08 ( 302) hydrogen bonds : angle 4.24181 / 2.93 ( 942) link_NAG-ASN : bond 0.00216 / 0.10 ( 3) link_NAG-ASN : angle 1.50610 / 0.85 ( 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 100 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.286 Fit side-chains REVERT: A 172 LYS cc_start: 0.8342 (tppt) cc_final: 0.8054 (mttp) REVERT: A 256 MET cc_start: 0.8509 (mmm) cc_final: 0.8297 (tpp) REVERT: B 118 LYS cc_start: 0.7905 (mtpt) cc_final: 0.7307 (mmtp) REVERT: B 172 LYS cc_start: 0.8346 (mttp) cc_final: 0.7846 (mtpt) REVERT: B 320 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8743 (mm) REVERT: C 74 ILE cc_start: 0.7862 (tp) cc_final: 0.7539 (tt) REVERT: C 108 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8558 (ptp) REVERT: C 172 LYS cc_start: 0.8360 (tppt) cc_final: 0.7709 (mttt) REVERT: C 320 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8691 (mm) outliers start: 28 outliers final: 19 residues processed: 93 average time/residue: 0.0971 time to fit residues: 12.1899 Evaluate side-chains 93 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 ILE 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 291 VAL Chi-restraints excluded: chain B residue 63 VAL 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 259 GLN 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 108 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 57 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN ** C 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 = 0.3688 r_free = 0.3688 target = 0.157643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.112637 restraints weight = 7574.068| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.08 r_work: 0.2922 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7641 Z= 0.176 Angle : 0.606 8.089 10437 Z= 0.306 Chirality : 0.045 0.154 1185 Planarity : 0.004 0.035 1350 Dihedral : 6.381 42.309 1071 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.01 % Allowed : 19.61 % Favored : 77.39 % 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 are not related in a simple way. whole: 0.20 (0.27), residues: 942 helix: 0.92 (0.41), residues: 198 sheet: 0.69 (0.27), residues: 306 loop : -0.58 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 280 TYR 0.015 0.001 TYR C 318 PHE 0.011 0.001 PHE A 299 TRP 0.010 0.002 TRP A 167 HIS 0.001 0.001 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 ( 7623) covalent geometry : angle 0.59713 / 0.30 (10398) SS BOND : bond 0.00397 / 0.30 ( 15) SS BOND : angle 1.96133 / 1.41 ( 30) hydrogen bonds : bond 0.03025 / 1.97 ( 302) hydrogen bonds : angle 4.16213 / 2.87 ( 942) link_NAG-ASN : bond 0.00095 / 0.04 ( 3) link_NAG-ASN : angle 1.29886 / 0.73 ( 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 91 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.271 Fit side-chains REVERT: A 172 LYS cc_start: 0.8311 (tppt) cc_final: 0.8018 (mttp) REVERT: A 256 MET cc_start: 0.8447 (mmm) cc_final: 0.8175 (tpp) REVERT: B 118 LYS cc_start: 0.7854 (mtpt) cc_final: 0.7289 (mmtp) REVERT: B 172 LYS cc_start: 0.8372 (mttp) cc_final: 0.7881 (mtpt) REVERT: B 320 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8736 (mm) REVERT: C 108 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8582 (ptp) REVERT: C 172 LYS cc_start: 0.8366 (tppt) cc_final: 0.7728 (mttt) REVERT: C 320 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8675 (mm) outliers start: 23 outliers final: 18 residues processed: 85 average time/residue: 0.1054 time to fit residues: 11.8540 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 : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 ILE 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 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 129 CYS 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 B residue 320 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 108 MET 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: 0.9980 chunk 63 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.161391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.113623 restraints weight = 7509.339| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.21 r_work: 0.3019 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1855 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= 0.108 Angle : 0.538 8.430 10437 Z= 0.270 Chirality : 0.043 0.135 1185 Planarity : 0.004 0.036 1350 Dihedral : 6.103 43.961 1071 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.88 % Allowed : 20.00 % 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 are not related in a simple way. whole: 0.54 (0.27), residues: 942 helix: 1.10 (0.41), residues: 198 sheet: 0.86 (0.27), residues: 330 loop : -0.37 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 85 TYR 0.012 0.001 TYR C 318 PHE 0.010 0.001 PHE A 297 TRP 0.015 0.001 TRP A 167 HIS 0.001 0.000 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 7623) covalent geometry : angle 0.53233 / 0.27 (10398) SS BOND : bond 0.00324 / 0.25 ( 15) SS BOND : angle 1.53210 / 1.10 ( 30) hydrogen bonds : bond 0.02525 / 1.66 ( 302) hydrogen bonds : angle 3.94326 / 2.71 ( 942) link_NAG-ASN : bond 0.00150 / 0.07 ( 3) link_NAG-ASN : angle 0.87007 / 0.48 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1902.63 seconds wall clock time: 33 minutes 19.88 seconds (1999.88 seconds total)