Starting phenix.real_space_refine on Sat Dec 28 03:13:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jv6_36669/12_2024/8jv6_36669.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jv6_36669/12_2024/8jv6_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_36669/12_2024/8jv6_36669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jv6_36669/12_2024/8jv6_36669.map" model { file = "/net/cci-nas-00/data/ceres_data/8jv6_36669/12_2024/8jv6_36669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jv6_36669/12_2024/8jv6_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-5532/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: 4.86, per 1000 atoms: 0.65 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: 1.79 Conformation dependent library (CDL) restraints added in 1.1 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: 0.90 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: 2.32 Time building geometry restraints manager: 2.07 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: 0.720 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.660 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.180 ------------------------------------------------------------------------------- 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 7623 Z= 0.323 Angle : 0.751 18.670 10398 Z= 0.344 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 *********************** 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 : 0.809 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: 0.2277 time to fit residues: 22.6660 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 : 0.793 ------------------------------------------------------------------------------- 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: 1.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7623 Z= 0.200 Angle : 0.539 6.548 10398 Z= 0.274 Chirality : 0.044 0.149 1185 Planarity : 0.004 0.054 1350 Dihedral : 8.972 58.789 1323 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.48 % Allowed : 16.86 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.65 (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 *********************** 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 98 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.717 Fit side-chains REVERT: A 172 LYS cc_start: 0.8221 (tppt) cc_final: 0.7797 (mttp) REVERT: A 259 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8368 (pt0) REVERT: A 285 LYS cc_start: 0.8392 (mttt) cc_final: 0.7950 (mttp) REVERT: A 320 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8659 (mm) REVERT: B 320 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8943 (mm) REVERT: B 346 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7215 (mp) REVERT: C 320 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8753 (mm) outliers start: 19 outliers final: 6 residues processed: 94 average time/residue: 0.2100 time to fit residues: 26.6119 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 : 0.825 ------------------------------------------------------------------------------- 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 46 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 70 optimal weight: 30.0000 chunk 57 optimal weight: 0.0060 chunk 23 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 chunk 91 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 0.0370 overall best weight: 0.4274 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 7623 Z= 0.158 Angle : 0.506 8.256 10398 Z= 0.258 Chirality : 0.043 0.136 1185 Planarity : 0.004 0.043 1350 Dihedral : 8.213 59.116 1323 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.27 % Allowed : 17.52 % Favored : 79.22 % 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: 0.83 (0.27), residues: 942 helix: 1.81 (0.44), residues: 162 sheet: 0.95 (0.27), residues: 318 loop : -0.15 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 167 HIS 0.001 0.000 HIS A 132 PHE 0.008 0.001 PHE A 299 TYR 0.014 0.001 TYR A 318 ARG 0.003 0.000 ARG C 148 *********************** 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 100 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.787 Fit side-chains REVERT: A 172 LYS cc_start: 0.8206 (tppt) cc_final: 0.7847 (mttp) REVERT: A 285 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7792 (mttp) REVERT: B 118 LYS cc_start: 0.7715 (mtmt) cc_final: 0.7358 (mmtp) REVERT: B 172 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7749 (mtpt) REVERT: B 320 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8949 (mm) REVERT: C 108 MET cc_start: 0.8824 (ppp) cc_final: 0.8396 (ptt) REVERT: C 320 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8709 (mm) REVERT: C 346 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7391 (mp) outliers start: 25 outliers final: 8 residues processed: 95 average time/residue: 0.1955 time to fit residues: 25.4774 Evaluate side-chains 81 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 B residue 63 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 83 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 0.0000 chunk 40 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 0.0020 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN B 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7623 Z= 0.167 Angle : 0.517 8.296 10398 Z= 0.259 Chirality : 0.043 0.132 1185 Planarity : 0.003 0.039 1350 Dihedral : 7.725 59.600 1323 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.01 % Allowed : 18.43 % Favored : 78.56 % 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: 0.60 (0.27), residues: 942 helix: 1.17 (0.43), residues: 180 sheet: 0.98 (0.27), residues: 318 loop : -0.31 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 167 HIS 0.001 0.000 HIS C 132 PHE 0.009 0.001 PHE A 102 TYR 0.013 0.001 TYR C 318 ARG 0.003 0.000 ARG C 148 *********************** 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 93 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.905 Fit side-chains REVERT: A 172 LYS cc_start: 0.8213 (tppt) cc_final: 0.7856 (mttp) REVERT: B 320 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8935 (mm) REVERT: B 346 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7284 (mp) REVERT: C 108 MET cc_start: 0.8824 (ppp) cc_final: 0.8368 (ptt) REVERT: C 320 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8713 (mm) REVERT: C 346 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7263 (mp) outliers start: 23 outliers final: 10 residues processed: 87 average time/residue: 0.1916 time to fit residues: 22.8460 Evaluate side-chains 82 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 63 VAL 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 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 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 74 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7623 Z= 0.325 Angle : 0.623 8.535 10398 Z= 0.315 Chirality : 0.046 0.153 1185 Planarity : 0.004 0.035 1350 Dihedral : 7.419 52.823 1323 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.79 % Allowed : 18.56 % 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 (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: 0.38 (0.27), residues: 942 helix: 0.91 (0.41), residues: 198 sheet: 0.75 (0.27), residues: 321 loop : -0.39 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 262 HIS 0.001 0.001 HIS C 132 PHE 0.012 0.002 PHE C 299 TYR 0.016 0.002 TYR C 318 ARG 0.003 0.000 ARG A 280 *********************** 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: 29 poor density : 78 time to evaluate : 0.960 Fit side-chains REVERT: A 172 LYS cc_start: 0.8268 (tppt) cc_final: 0.7963 (mttp) REVERT: A 256 MET cc_start: 0.8596 (mmm) cc_final: 0.8303 (tpp) REVERT: B 320 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8899 (mm) REVERT: C 108 MET cc_start: 0.8930 (ppp) cc_final: 0.8441 (ptt) REVERT: C 214 SER cc_start: 0.8050 (p) cc_final: 0.7799 (t) REVERT: C 285 LYS cc_start: 0.8173 (mttt) cc_final: 0.7804 (mttm) REVERT: C 320 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8780 (mm) outliers start: 29 outliers final: 12 residues processed: 103 average time/residue: 0.2057 time to fit residues: 28.8234 Evaluate side-chains 82 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 291 VAL Chi-restraints excluded: chain B residue 63 VAL 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 320 ILE 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 30 optimal weight: 6.9990 chunk 80 optimal weight: 0.0370 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7623 Z= 0.201 Angle : 0.561 8.381 10398 Z= 0.282 Chirality : 0.044 0.137 1185 Planarity : 0.004 0.032 1350 Dihedral : 7.099 45.829 1323 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.88 % Allowed : 19.22 % 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: 0.52 (0.27), residues: 942 helix: 1.13 (0.42), residues: 198 sheet: 0.84 (0.27), residues: 321 loop : -0.36 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 167 HIS 0.001 0.000 HIS B 132 PHE 0.010 0.001 PHE A 297 TYR 0.013 0.001 TYR C 318 ARG 0.004 0.000 ARG B 148 *********************** 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: 22 poor density : 72 time to evaluate : 0.757 Fit side-chains REVERT: A 118 LYS cc_start: 0.7813 (mtpt) cc_final: 0.7265 (mmtp) REVERT: A 172 LYS cc_start: 0.8283 (tppt) cc_final: 0.7998 (mttp) REVERT: B 118 LYS cc_start: 0.7873 (mtpt) cc_final: 0.7266 (mmtp) REVERT: B 320 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8885 (mm) REVERT: C 108 MET cc_start: 0.8915 (ppp) cc_final: 0.8416 (ptt) REVERT: C 172 LYS cc_start: 0.8201 (tppt) cc_final: 0.7577 (mttt) REVERT: C 320 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8730 (mm) outliers start: 22 outliers final: 15 residues processed: 86 average time/residue: 0.2136 time to fit residues: 24.6130 Evaluate side-chains 86 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 89 VAL 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 320 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 173 ILE 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 86 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 0.0060 chunk 89 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 7623 Z= 0.394 Angle : 0.659 9.903 10398 Z= 0.335 Chirality : 0.047 0.159 1185 Planarity : 0.004 0.032 1350 Dihedral : 7.301 42.131 1323 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.92 % Allowed : 18.30 % 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: 0.22 (0.27), residues: 942 helix: 0.92 (0.41), residues: 198 sheet: 0.70 (0.26), residues: 315 loop : -0.60 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 87 HIS 0.001 0.001 HIS C 132 PHE 0.014 0.002 PHE A 299 TYR 0.017 0.002 TYR C 318 ARG 0.003 0.001 ARG A 280 *********************** 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: 30 poor density : 72 time to evaluate : 0.744 Fit side-chains REVERT: A 172 LYS cc_start: 0.8340 (tppt) cc_final: 0.8052 (mttp) REVERT: A 256 MET cc_start: 0.8596 (mmm) cc_final: 0.8365 (tpp) REVERT: A 259 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8321 (pt0) REVERT: B 118 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7322 (mmtp) REVERT: B 172 LYS cc_start: 0.8334 (mttp) cc_final: 0.7851 (mtpt) REVERT: B 320 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8878 (mm) REVERT: C 86 ILE cc_start: 0.8330 (tt) cc_final: 0.7945 (mm) REVERT: C 108 MET cc_start: 0.9044 (ppp) cc_final: 0.8531 (ptt) REVERT: C 172 LYS cc_start: 0.8286 (tppt) cc_final: 0.7673 (mttt) REVERT: C 320 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8799 (mm) outliers start: 30 outliers final: 17 residues processed: 96 average time/residue: 0.2140 time to fit residues: 27.6674 Evaluate side-chains 89 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 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 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 66 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 70 optimal weight: 0.0770 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7623 Z= 0.179 Angle : 0.561 7.786 10398 Z= 0.282 Chirality : 0.044 0.141 1185 Planarity : 0.004 0.033 1350 Dihedral : 6.907 43.688 1323 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.41 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 (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: 0.44 (0.27), residues: 942 helix: 1.17 (0.42), residues: 198 sheet: 0.76 (0.27), residues: 321 loop : -0.45 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 167 HIS 0.001 0.000 HIS B 132 PHE 0.010 0.001 PHE B 297 TYR 0.012 0.001 TYR C 318 ARG 0.003 0.000 ARG C 85 *********************** 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: 23 poor density : 71 time to evaluate : 0.806 Fit side-chains REVERT: A 172 LYS cc_start: 0.8329 (tppt) cc_final: 0.8009 (mttp) REVERT: A 256 MET cc_start: 0.8509 (mmm) cc_final: 0.8252 (tpp) REVERT: A 259 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8276 (pt0) REVERT: B 118 LYS cc_start: 0.7910 (mtpt) cc_final: 0.7308 (mmtp) REVERT: B 172 LYS cc_start: 0.8352 (mttp) cc_final: 0.7880 (mtpt) REVERT: B 320 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8867 (mm) REVERT: C 108 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8586 (ptp) REVERT: C 172 LYS cc_start: 0.8256 (tppt) cc_final: 0.7664 (mttt) REVERT: C 320 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8727 (mm) outliers start: 23 outliers final: 16 residues processed: 89 average time/residue: 0.2283 time to fit residues: 27.0625 Evaluate side-chains 86 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 overall best weight: 1.0388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7623 Z= 0.236 Angle : 0.573 8.337 10398 Z= 0.289 Chirality : 0.044 0.145 1185 Planarity : 0.004 0.033 1350 Dihedral : 6.827 43.192 1323 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.53 % Allowed : 19.35 % 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: 0.42 (0.27), residues: 942 helix: 1.16 (0.42), residues: 198 sheet: 0.76 (0.27), residues: 321 loop : -0.47 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 167 HIS 0.001 0.000 HIS C 132 PHE 0.011 0.001 PHE A 299 TYR 0.014 0.001 TYR C 318 ARG 0.002 0.000 ARG A 148 *********************** 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 93 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.814 Fit side-chains REVERT: A 172 LYS cc_start: 0.8333 (tppt) cc_final: 0.8004 (mttp) REVERT: A 256 MET cc_start: 0.8562 (mmm) cc_final: 0.8289 (tpp) REVERT: A 259 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8272 (pt0) REVERT: B 118 LYS cc_start: 0.7914 (mtpt) cc_final: 0.7322 (mmtp) REVERT: B 172 LYS cc_start: 0.8321 (mttp) cc_final: 0.7832 (mtpt) REVERT: B 320 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8910 (mm) REVERT: C 108 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8586 (ptp) REVERT: C 172 LYS cc_start: 0.8232 (tppt) cc_final: 0.7632 (mttt) REVERT: C 289 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8121 (t0) REVERT: C 320 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8717 (mm) outliers start: 27 outliers final: 18 residues processed: 89 average time/residue: 0.2151 time to fit residues: 25.7216 Evaluate side-chains 87 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 182 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7623 Z= 0.229 Angle : 0.568 7.929 10398 Z= 0.287 Chirality : 0.044 0.144 1185 Planarity : 0.004 0.035 1350 Dihedral : 6.791 43.227 1323 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.40 % Allowed : 19.08 % 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 (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: 0.44 (0.27), residues: 942 helix: 1.17 (0.42), residues: 198 sheet: 0.79 (0.27), residues: 321 loop : -0.47 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 167 HIS 0.001 0.000 HIS C 132 PHE 0.011 0.001 PHE A 299 TYR 0.014 0.001 TYR C 318 ARG 0.002 0.000 ARG A 148 ********************** 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 93 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.766 Fit side-chains REVERT: A 172 LYS cc_start: 0.8286 (tppt) cc_final: 0.7962 (mttp) REVERT: A 256 MET cc_start: 0.8567 (mmm) cc_final: 0.8292 (tpp) REVERT: A 259 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: B 118 LYS cc_start: 0.7891 (mtpt) cc_final: 0.7299 (mmtp) REVERT: B 172 LYS cc_start: 0.8298 (mttp) cc_final: 0.7823 (mtpt) REVERT: B 320 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8910 (mm) REVERT: C 108 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8587 (ptp) REVERT: C 172 LYS cc_start: 0.8234 (tppt) cc_final: 0.7639 (mttt) REVERT: C 320 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8723 (mm) outliers start: 26 outliers final: 21 residues processed: 88 average time/residue: 0.2152 time to fit residues: 25.3239 Evaluate side-chains 91 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 119 CYS Chi-restraints excluded: chain B residue 129 CYS 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 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 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 22 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 0.0370 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.160685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113438 restraints weight = 7496.804| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.21 r_work: 0.2967 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7623 Z= 0.185 Angle : 0.535 7.331 10398 Z= 0.270 Chirality : 0.043 0.136 1185 Planarity : 0.004 0.035 1350 Dihedral : 6.476 43.915 1323 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.53 % Allowed : 18.82 % 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 (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: 0.36 (0.27), residues: 942 helix: 0.69 (0.40), residues: 216 sheet: 0.94 (0.27), residues: 324 loop : -0.54 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 167 HIS 0.001 0.000 HIS B 132 PHE 0.010 0.001 PHE A 297 TYR 0.012 0.001 TYR C 318 ARG 0.002 0.000 ARG C 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1756.58 seconds wall clock time: 33 minutes 1.68 seconds (1981.68 seconds total)