Starting phenix.real_space_refine on Fri Jul 25 11:42:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jv6_36669/07_2025/8jv6_36669.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jv6_36669/07_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_36669/07_2025/8jv6_36669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jv6_36669/07_2025/8jv6_36669.map" model { file = "/net/cci-nas-00/data/ceres_data/8jv6_36669/07_2025/8jv6_36669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jv6_36669/07_2025/8jv6_36669.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} 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: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} 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: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} 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: 5.41, per 1000 atoms: 0.73 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: 2.27 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.00 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: 2.12 Time building geometry restraints manager: 2.48 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 358 or resid 401 through 403)) selection = (chain 'B' and (resid 43 through 358 or resid 401 through 403)) selection = (chain 'C' and (resid 43 through 358 or resid 401 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: 1.400 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.960 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP A 167 HIS 0.001 0.000 HIS A 132 PHE 0.011 0.001 PHE A 299 TYR 0.016 0.001 TYR A 53 ARG 0.009 0.001 ARG A 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00010 ( 3) link_NAG-ASN : angle 0.93770 ( 9) hydrogen bonds : bond 0.13302 ( 302) hydrogen bonds : angle 5.36628 ( 942) SS BOND : bond 0.00361 ( 15) SS BOND : angle 1.88311 ( 30) covalent geometry : bond 0.00488 ( 7623) covalent geometry : angle 0.75134 (10398) *********************** 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 : 0.799 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: 0.2259 time to fit residues: 22.4453 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 : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 4.9990 chunk 70 optimal weight: 40.0000 chunk 39 optimal weight: 40.0000 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.172930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.112557 restraints weight = 7491.902| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.92 r_work: 0.3057 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.0585 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= 0.126 Angle : 0.546 6.593 10437 Z= 0.277 Chirality : 0.044 0.148 1185 Planarity : 0.004 0.054 1350 Dihedral : 8.957 58.593 1323 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.27), residues: 942 helix: 1.31 (0.42), residues: 180 sheet: 0.78 (0.27), residues: 324 loop : -0.12 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 167 HIS 0.001 0.000 HIS B 132 PHE 0.010 0.001 PHE A 297 TYR 0.014 0.001 TYR C 318 ARG 0.004 0.000 ARG C 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 3) link_NAG-ASN : angle 0.99658 ( 9) hydrogen bonds : bond 0.03119 ( 302) hydrogen bonds : angle 4.33822 ( 942) SS BOND : bond 0.00481 ( 15) SS BOND : angle 1.77190 ( 30) covalent geometry : bond 0.00303 ( 7623) covalent geometry : angle 0.53783 (10398) *********************** 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 99 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.767 Fit side-chains REVERT: A 172 LYS cc_start: 0.8171 (tppt) cc_final: 0.7778 (mttp) REVERT: A 259 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8297 (pt0) REVERT: A 285 LYS cc_start: 0.8350 (mttt) cc_final: 0.7843 (mttp) REVERT: A 320 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8489 (mm) REVERT: B 320 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8813 (mm) REVERT: B 346 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.7006 (mp) REVERT: C 320 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8629 (mm) outliers start: 20 outliers final: 6 residues processed: 94 average time/residue: 0.2066 time to fit residues: 26.2712 Evaluate side-chains 83 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 37 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.160882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.115185 restraints weight = 7593.139| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.14 r_work: 0.2942 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7641 Z= 0.151 Angle : 0.566 10.334 10437 Z= 0.287 Chirality : 0.044 0.156 1185 Planarity : 0.004 0.043 1350 Dihedral : 8.441 59.912 1323 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.53 % Allowed : 18.17 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 942 helix: 0.84 (0.41), residues: 198 sheet: 0.77 (0.27), residues: 324 loop : -0.33 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 167 HIS 0.001 0.001 HIS C 132 PHE 0.010 0.001 PHE A 299 TYR 0.018 0.001 TYR A 318 ARG 0.003 0.000 ARG C 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 3) link_NAG-ASN : angle 1.07297 ( 9) hydrogen bonds : bond 0.03008 ( 302) hydrogen bonds : angle 4.22539 ( 942) SS BOND : bond 0.00450 ( 15) SS BOND : angle 1.80065 ( 30) covalent geometry : bond 0.00373 ( 7623) covalent geometry : angle 0.55777 (10398) *********************** 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: 27 poor density : 77 time to evaluate : 0.784 Fit side-chains REVERT: A 172 LYS cc_start: 0.8249 (tppt) cc_final: 0.7896 (mttp) REVERT: A 259 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8394 (pt0) REVERT: B 118 LYS cc_start: 0.7798 (mtmt) cc_final: 0.7313 (mmtp) REVERT: B 172 LYS cc_start: 0.8318 (ttmm) cc_final: 0.7784 (mtpt) REVERT: B 320 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8803 (mm) REVERT: C 108 MET cc_start: 0.8807 (ppp) cc_final: 0.8292 (ptt) REVERT: C 320 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8650 (mm) REVERT: C 346 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7222 (mp) outliers start: 27 outliers final: 11 residues processed: 100 average time/residue: 0.2098 time to fit residues: 28.3394 Evaluate side-chains 87 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN ** 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 = 0.3766 r_free = 0.3766 target = 0.164558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.118565 restraints weight = 7474.050| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.13 r_work: 0.2976 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1080 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= 0.120 Angle : 0.539 7.384 10437 Z= 0.272 Chirality : 0.044 0.135 1185 Planarity : 0.004 0.037 1350 Dihedral : 7.729 57.197 1323 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.14 % Allowed : 19.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.27), residues: 942 helix: 1.17 (0.43), residues: 180 sheet: 0.89 (0.27), residues: 318 loop : -0.36 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 167 HIS 0.001 0.000 HIS B 132 PHE 0.009 0.001 PHE A 299 TYR 0.014 0.001 TYR A 318 ARG 0.002 0.000 ARG A 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00088 ( 3) link_NAG-ASN : angle 1.09752 ( 9) hydrogen bonds : bond 0.02691 ( 302) hydrogen bonds : angle 4.00047 ( 942) SS BOND : bond 0.00380 ( 15) SS BOND : angle 1.75642 ( 30) covalent geometry : bond 0.00290 ( 7623) covalent geometry : angle 0.53117 (10398) *********************** 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 98 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.760 Fit side-chains REVERT: A 172 LYS cc_start: 0.8263 (tppt) cc_final: 0.7891 (mttp) REVERT: A 259 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8388 (pt0) REVERT: C 108 MET cc_start: 0.8815 (ppp) cc_final: 0.8291 (ptt) REVERT: C 320 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8635 (mm) REVERT: C 346 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7183 (mp) outliers start: 24 outliers final: 11 residues processed: 90 average time/residue: 0.2159 time to fit residues: 26.0737 Evaluate side-chains 85 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 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 B residue 63 VAL Chi-restraints excluded: chain B residue 89 VAL 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 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 52 optimal weight: 0.0030 chunk 91 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 overall best weight: 1.0994 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.159657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115814 restraints weight = 7457.738| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.96 r_work: 0.2965 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7641 Z= 0.148 Angle : 0.565 6.529 10437 Z= 0.286 Chirality : 0.045 0.144 1185 Planarity : 0.004 0.034 1350 Dihedral : 7.138 50.744 1323 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.53 % Allowed : 18.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.27), residues: 942 helix: 1.01 (0.41), residues: 198 sheet: 0.76 (0.27), residues: 324 loop : -0.44 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 262 HIS 0.001 0.001 HIS C 132 PHE 0.011 0.001 PHE A 299 TYR 0.016 0.001 TYR A 318 ARG 0.003 0.000 ARG B 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 3) link_NAG-ASN : angle 1.38511 ( 9) hydrogen bonds : bond 0.02866 ( 302) hydrogen bonds : angle 4.06693 ( 942) SS BOND : bond 0.00424 ( 15) SS BOND : angle 1.70720 ( 30) covalent geometry : bond 0.00364 ( 7623) covalent geometry : angle 0.55717 (10398) *********************** 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 107 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.699 Fit side-chains REVERT: A 165 LEU cc_start: 0.7992 (mm) cc_final: 0.7788 (mp) REVERT: A 172 LYS cc_start: 0.8264 (tppt) cc_final: 0.7952 (mttp) REVERT: A 259 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8396 (pt0) REVERT: B 346 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7386 (mp) REVERT: C 108 MET cc_start: 0.8840 (ppp) cc_final: 0.8323 (ptt) REVERT: C 214 SER cc_start: 0.7902 (p) cc_final: 0.7635 (t) REVERT: C 320 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8646 (mm) outliers start: 27 outliers final: 15 residues processed: 102 average time/residue: 0.1947 time to fit residues: 26.8848 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 : 0.695 ------------------------------------------------------------------------------- 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 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 221 VAL Chi-restraints excluded: chain B residue 278 THR 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 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 79 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 42 optimal weight: 30.0000 chunk 58 optimal weight: 3.9990 chunk 49 optimal weight: 0.0060 chunk 85 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- 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** C 122 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 = 0.3698 r_free = 0.3698 target = 0.158511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.113127 restraints weight = 7604.590| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.19 r_work: 0.2887 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 7641 Z= 0.188 Angle : 0.616 7.332 10437 Z= 0.312 Chirality : 0.046 0.157 1185 Planarity : 0.004 0.031 1350 Dihedral : 7.177 42.847 1323 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.53 % Allowed : 19.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.27), residues: 942 helix: 0.95 (0.41), residues: 198 sheet: 0.71 (0.27), residues: 321 loop : -0.48 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 167 HIS 0.001 0.001 HIS C 132 PHE 0.012 0.002 PHE A 299 TYR 0.016 0.001 TYR A 318 ARG 0.002 0.000 ARG A 280 Details of bonding type rmsd link_NAG-ASN : bond 0.00094 ( 3) link_NAG-ASN : angle 1.60601 ( 9) hydrogen bonds : bond 0.03096 ( 302) hydrogen bonds : angle 4.22106 ( 942) SS BOND : bond 0.00403 ( 15) SS BOND : angle 2.17849 ( 30) covalent geometry : bond 0.00469 ( 7623) covalent geometry : angle 0.60452 (10398) *********************** 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 94 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.816 Fit side-chains REVERT: A 172 LYS cc_start: 0.8316 (tppt) cc_final: 0.8029 (mttp) REVERT: A 256 MET cc_start: 0.8475 (mmm) cc_final: 0.8196 (tpp) REVERT: A 259 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8408 (pt0) REVERT: B 118 LYS cc_start: 0.7924 (mtpt) cc_final: 0.7317 (mmtp) REVERT: C 108 MET cc_start: 0.8923 (ppp) cc_final: 0.8554 (ptp) REVERT: C 172 LYS cc_start: 0.8283 (tppt) cc_final: 0.7604 (mttt) REVERT: C 320 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8674 (mm) outliers start: 27 outliers final: 20 residues processed: 88 average time/residue: 0.2240 time to fit residues: 26.3506 Evaluate side-chains 87 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 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 116 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.0270 chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.161977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.116915 restraints weight = 7587.448| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.07 r_work: 0.2959 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7641 Z= 0.119 Angle : 0.546 7.149 10437 Z= 0.276 Chirality : 0.044 0.138 1185 Planarity : 0.004 0.029 1350 Dihedral : 6.732 43.855 1323 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.18 % Allowed : 18.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 942 helix: 1.11 (0.41), residues: 198 sheet: 0.90 (0.27), residues: 318 loop : -0.46 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 167 HIS 0.001 0.000 HIS C 132 PHE 0.010 0.001 PHE A 297 TYR 0.013 0.001 TYR C 318 ARG 0.003 0.000 ARG B 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00064 ( 3) link_NAG-ASN : angle 1.28626 ( 9) hydrogen bonds : bond 0.02621 ( 302) hydrogen bonds : angle 3.99577 ( 942) SS BOND : bond 0.00328 ( 15) SS BOND : angle 1.73347 ( 30) covalent geometry : bond 0.00289 ( 7623) covalent geometry : angle 0.53766 (10398) *********************** 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 102 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.770 Fit side-chains REVERT: A 172 LYS cc_start: 0.8331 (tppt) cc_final: 0.8023 (mttp) REVERT: A 256 MET cc_start: 0.8410 (mmm) cc_final: 0.8180 (tpp) REVERT: A 259 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8435 (pt0) REVERT: B 118 LYS cc_start: 0.7875 (mtpt) cc_final: 0.7303 (mmtp) REVERT: B 172 LYS cc_start: 0.8331 (mttp) cc_final: 0.7871 (mtpt) REVERT: B 320 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8715 (mm) REVERT: C 108 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8505 (ptp) REVERT: C 172 LYS cc_start: 0.8350 (tppt) cc_final: 0.7702 (mttt) REVERT: C 182 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7711 (mt) REVERT: C 289 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8052 (t0) REVERT: C 320 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8635 (mm) outliers start: 32 outliers final: 17 residues processed: 95 average time/residue: 0.2115 time to fit residues: 26.9647 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 : 0.756 ------------------------------------------------------------------------------- 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 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 129 CYS Chi-restraints excluded: chain B residue 196 ILE 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 182 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 52 optimal weight: 5.9990 chunk 44 optimal weight: 0.0020 chunk 42 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- 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 C 58 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 = 0.3695 r_free = 0.3695 target = 0.158307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.112308 restraints weight = 7658.968| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.26 r_work: 0.2899 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7641 Z= 0.191 Angle : 0.613 7.464 10437 Z= 0.311 Chirality : 0.046 0.158 1185 Planarity : 0.004 0.032 1350 Dihedral : 6.967 42.570 1323 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.92 % Allowed : 18.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.27), residues: 942 helix: 0.98 (0.41), residues: 198 sheet: 0.72 (0.27), residues: 321 loop : -0.50 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 262 HIS 0.001 0.001 HIS C 132 PHE 0.012 0.002 PHE A 299 TYR 0.022 0.001 TYR A 318 ARG 0.003 0.000 ARG A 280 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 3) link_NAG-ASN : angle 1.65489 ( 9) hydrogen bonds : bond 0.03070 ( 302) hydrogen bonds : angle 4.17989 ( 942) SS BOND : bond 0.00423 ( 15) SS BOND : angle 2.09316 ( 30) covalent geometry : bond 0.00475 ( 7623) covalent geometry : angle 0.60137 (10398) *********************** 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: 30 poor density : 64 time to evaluate : 0.760 Fit side-chains REVERT: A 172 LYS cc_start: 0.8343 (tppt) cc_final: 0.8046 (mttp) REVERT: A 256 MET cc_start: 0.8521 (mmm) cc_final: 0.8302 (tpp) REVERT: A 259 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8418 (pt0) REVERT: B 118 LYS cc_start: 0.7795 (mtpt) cc_final: 0.7168 (mmtp) REVERT: B 172 LYS cc_start: 0.8358 (mttp) cc_final: 0.7877 (mtpt) REVERT: B 320 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8664 (mm) REVERT: C 108 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8402 (ptt) REVERT: C 172 LYS cc_start: 0.8308 (tppt) cc_final: 0.7662 (mttt) REVERT: C 320 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8703 (mm) outliers start: 30 outliers final: 22 residues processed: 90 average time/residue: 0.2206 time to fit residues: 26.5588 Evaluate side-chains 89 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 259 GLN Chi-restraints excluded: chain A residue 271 SER 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 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 182 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 278 THR 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 43 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 ** 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 = 0.3698 r_free = 0.3698 target = 0.158639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.112877 restraints weight = 7633.287| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.21 r_work: 0.2906 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7641 Z= 0.183 Angle : 0.601 7.384 10437 Z= 0.306 Chirality : 0.045 0.157 1185 Planarity : 0.004 0.037 1350 Dihedral : 7.015 42.479 1323 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.18 % Allowed : 18.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 942 helix: 0.93 (0.41), residues: 198 sheet: 0.67 (0.27), residues: 321 loop : -0.56 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 167 HIS 0.001 0.001 HIS C 132 PHE 0.012 0.002 PHE A 299 TYR 0.022 0.001 TYR A 318 ARG 0.002 0.000 ARG B 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00076 ( 3) link_NAG-ASN : angle 1.53539 ( 9) hydrogen bonds : bond 0.03015 ( 302) hydrogen bonds : angle 4.17154 ( 942) SS BOND : bond 0.00374 ( 15) SS BOND : angle 1.96546 ( 30) covalent geometry : bond 0.00457 ( 7623) covalent geometry : angle 0.59145 (10398) *********************** 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 98 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 0.805 Fit side-chains REVERT: A 172 LYS cc_start: 0.8300 (tppt) cc_final: 0.8003 (mttp) REVERT: A 256 MET cc_start: 0.8479 (mmm) cc_final: 0.8260 (tpp) REVERT: A 259 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8421 (pt0) REVERT: B 118 LYS cc_start: 0.7936 (mtpt) cc_final: 0.7324 (mmtp) REVERT: B 172 LYS cc_start: 0.8384 (mttp) cc_final: 0.7907 (mtpt) REVERT: B 320 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8695 (mm) REVERT: C 108 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8388 (ptt) REVERT: C 172 LYS cc_start: 0.8354 (tppt) cc_final: 0.7722 (mttt) REVERT: C 320 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8690 (mm) outliers start: 32 outliers final: 25 residues processed: 93 average time/residue: 0.2112 time to fit residues: 26.4705 Evaluate side-chains 94 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 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 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 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 278 THR 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 7 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.159483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.114019 restraints weight = 7633.573| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.16 r_work: 0.2911 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7641 Z= 0.131 Angle : 0.566 7.340 10437 Z= 0.287 Chirality : 0.044 0.145 1185 Planarity : 0.004 0.038 1350 Dihedral : 6.862 43.114 1323 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.79 % Allowed : 19.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.27), residues: 942 helix: 1.03 (0.41), residues: 198 sheet: 0.76 (0.27), residues: 321 loop : -0.49 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 167 HIS 0.001 0.000 HIS C 132 PHE 0.011 0.001 PHE A 299 TYR 0.018 0.001 TYR A 318 ARG 0.001 0.000 ARG A 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00020 ( 3) link_NAG-ASN : angle 1.35963 ( 9) hydrogen bonds : bond 0.02756 ( 302) hydrogen bonds : angle 4.05949 ( 942) SS BOND : bond 0.00321 ( 15) SS BOND : angle 1.73701 ( 30) covalent geometry : bond 0.00320 ( 7623) covalent geometry : angle 0.55765 (10398) ********************** 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 96 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.795 Fit side-chains REVERT: A 172 LYS cc_start: 0.8267 (tppt) cc_final: 0.7956 (mttp) REVERT: A 256 MET cc_start: 0.8450 (mmm) cc_final: 0.8193 (tpp) REVERT: A 259 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8389 (pt0) REVERT: B 118 LYS cc_start: 0.7863 (mtpt) cc_final: 0.7265 (mmtp) REVERT: B 172 LYS cc_start: 0.8327 (mttp) cc_final: 0.7861 (mtpt) REVERT: B 320 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8720 (mm) REVERT: C 108 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8382 (ptt) REVERT: C 172 LYS cc_start: 0.8284 (tppt) cc_final: 0.7637 (mttt) REVERT: C 320 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8652 (mm) outliers start: 29 outliers final: 23 residues processed: 91 average time/residue: 0.2128 time to fit residues: 26.2166 Evaluate side-chains 92 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 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 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 182 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 278 THR 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 52 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 0.0270 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 0.0870 chunk 42 optimal weight: 5.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.162013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.113739 restraints weight = 7521.329| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.46 r_work: 0.2955 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7641 Z= 0.105 Angle : 0.524 6.948 10437 Z= 0.266 Chirality : 0.043 0.136 1185 Planarity : 0.004 0.035 1350 Dihedral : 6.403 43.881 1323 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.53 % Allowed : 19.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.27), residues: 942 helix: 1.16 (0.42), residues: 198 sheet: 0.85 (0.27), residues: 315 loop : -0.47 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 167 HIS 0.001 0.000 HIS C 132 PHE 0.010 0.001 PHE B 297 TYR 0.015 0.001 TYR A 318 ARG 0.002 0.000 ARG A 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 3) link_NAG-ASN : angle 1.07925 ( 9) hydrogen bonds : bond 0.02466 ( 302) hydrogen bonds : angle 3.89671 ( 942) SS BOND : bond 0.00301 ( 15) SS BOND : angle 1.49403 ( 30) covalent geometry : bond 0.00249 ( 7623) covalent geometry : angle 0.51786 (10398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3877.43 seconds wall clock time: 67 minutes 4.09 seconds (4024.09 seconds total)