Starting phenix.real_space_refine on Sat Dec 28 02:25:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ct2_26978/12_2024/8ct2_26978.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ct2_26978/12_2024/8ct2_26978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ct2_26978/12_2024/8ct2_26978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ct2_26978/12_2024/8ct2_26978.map" model { file = "/net/cci-nas-00/data/ceres_data/8ct2_26978/12_2024/8ct2_26978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ct2_26978/12_2024/8ct2_26978.cif" } resolution = 3.1 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= 0.169 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 4884 2.51 5 N 1264 2.21 5 O 1296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 7464 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "B" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "C" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "A" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG D 234 " occ=0.48 ... (20 atoms not shown) pdb=" NH2BARG D 234 " occ=0.52 residue: pdb=" N AARG B 234 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 234 " occ=0.50 residue: pdb=" N AARG C 234 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 234 " occ=0.50 residue: pdb=" N AARG A 234 " occ=0.51 ... (20 atoms not shown) pdb=" NH2BARG A 234 " occ=0.49 Time building chain proxies: 8.65, per 1000 atoms: 1.16 Number of scatterers: 7464 At special positions: 0 Unit cell: (88.81, 89.64, 90.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1296 8.00 N 1264 7.00 C 4884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.8 seconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 76.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'D' and resid 3 through 6 Processing helix chain 'D' and resid 7 through 33 removed outlier: 3.575A pdb=" N TRP D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 37 Processing helix chain 'D' and resid 48 through 72 removed outlier: 5.754A pdb=" N HIS D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 86 Processing helix chain 'D' and resid 90 through 116 Processing helix chain 'D' and resid 134 through 157 Processing helix chain 'D' and resid 167 through 188 removed outlier: 5.736A pdb=" N ASP D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 204 removed outlier: 3.511A pdb=" N SER D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.676A pdb=" N LYS D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL D 244 " --> pdb=" O ASP D 240 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TRP D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 6 removed outlier: 3.603A pdb=" N LYS B 6 " --> pdb=" O SER B 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3 through 6' Processing helix chain 'B' and resid 7 through 33 removed outlier: 3.591A pdb=" N TRP B 11 " --> pdb=" O LYS B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 37 Processing helix chain 'B' and resid 48 through 72 removed outlier: 5.931A pdb=" N HIS B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 90 through 116 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 167 through 188 removed outlier: 5.706A pdb=" N ASP B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TYR B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 204 removed outlier: 3.586A pdb=" N SER B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 230 Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 237 through 248 removed outlier: 4.231A pdb=" N VAL B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TRP B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 6 removed outlier: 3.501A pdb=" N LYS C 6 " --> pdb=" O SER C 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3 through 6' Processing helix chain 'C' and resid 7 through 33 removed outlier: 3.770A pdb=" N TRP C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 37 Processing helix chain 'C' and resid 48 through 72 removed outlier: 6.024A pdb=" N HIS C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 90 through 116 Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 167 through 188 removed outlier: 5.637A pdb=" N ASP C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TYR C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 204 removed outlier: 3.791A pdb=" N SER C 199 " --> pdb=" O ARG C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 230 Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 237 through 248 removed outlier: 3.728A pdb=" N LYS C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL C 244 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TRP C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 6 Processing helix chain 'A' and resid 7 through 33 removed outlier: 3.505A pdb=" N TRP A 11 " --> pdb=" O LYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 37 Processing helix chain 'A' and resid 48 through 72 removed outlier: 5.902A pdb=" N HIS A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 Processing helix chain 'A' and resid 90 through 116 Processing helix chain 'A' and resid 134 through 157 Processing helix chain 'A' and resid 167 through 188 removed outlier: 5.609A pdb=" N ASP A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TYR A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 204 removed outlier: 3.557A pdb=" N SER A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 237 through 248 removed outlier: 3.705A pdb=" N LYS A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRP A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1599 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: 2.11 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2372 1.34 - 1.46: 1302 1.46 - 1.57: 3918 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 7620 Sorted by residual: bond pdb=" N ASN C 192 " pdb=" CA ASN C 192 " ideal model delta sigma weight residual 1.463 1.450 0.013 8.80e-03 1.29e+04 2.09e+00 bond pdb=" N ASN A 192 " pdb=" CA ASN A 192 " ideal model delta sigma weight residual 1.463 1.451 0.012 8.80e-03 1.29e+04 1.78e+00 bond pdb=" N ASN B 192 " pdb=" CA ASN B 192 " ideal model delta sigma weight residual 1.463 1.452 0.010 8.80e-03 1.29e+04 1.39e+00 bond pdb=" CG LEU D 112 " pdb=" CD2 LEU D 112 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.62e-01 bond pdb=" C ALA C 168 " pdb=" N PRO C 169 " ideal model delta sigma weight residual 1.335 1.349 -0.013 1.36e-02 5.41e+03 9.49e-01 ... (remaining 7615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 10197 1.76 - 3.51: 150 3.51 - 5.27: 37 5.27 - 7.03: 6 7.03 - 8.79: 2 Bond angle restraints: 10392 Sorted by residual: angle pdb=" C ILE A 191 " pdb=" N ASN A 192 " pdb=" CA ASN A 192 " ideal model delta sigma weight residual 122.26 126.52 -4.26 1.10e+00 8.26e-01 1.50e+01 angle pdb=" CA CYS D 189 " pdb=" CB CYS D 189 " pdb=" SG CYS D 189 " ideal model delta sigma weight residual 114.40 105.61 8.79 2.30e+00 1.89e-01 1.46e+01 angle pdb=" C ILE B 191 " pdb=" N ASN B 192 " pdb=" CA ASN B 192 " ideal model delta sigma weight residual 122.26 126.18 -3.92 1.10e+00 8.26e-01 1.27e+01 angle pdb=" C ILE C 191 " pdb=" N ASN C 192 " pdb=" CA ASN C 192 " ideal model delta sigma weight residual 122.26 126.14 -3.88 1.10e+00 8.26e-01 1.24e+01 angle pdb=" C ASP D 158 " pdb=" N ARG D 159 " pdb=" CA ARG D 159 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.99e+00 ... (remaining 10387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4293 17.91 - 35.82: 225 35.82 - 53.73: 46 53.73 - 71.64: 14 71.64 - 89.56: 6 Dihedral angle restraints: 4584 sinusoidal: 1808 harmonic: 2776 Sorted by residual: dihedral pdb=" CA LEU B 182 " pdb=" C LEU B 182 " pdb=" N ALA B 183 " pdb=" CA ALA B 183 " ideal model delta harmonic sigma weight residual -180.00 -156.02 -23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA LEU A 182 " pdb=" C LEU A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual 180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU D 182 " pdb=" C LEU D 182 " pdb=" N ALA D 183 " pdb=" CA ALA D 183 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 4581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 892 0.042 - 0.083: 324 0.083 - 0.125: 47 0.125 - 0.166: 4 0.166 - 0.208: 1 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CA CYS D 189 " pdb=" N CYS D 189 " pdb=" C CYS D 189 " pdb=" CB CYS D 189 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE D 191 " pdb=" CA ILE D 191 " pdb=" CG1 ILE D 191 " pdb=" CG2 ILE D 191 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.25e-01 chirality pdb=" CB ILE B 191 " pdb=" CA ILE B 191 " pdb=" CG1 ILE B 191 " pdb=" CG2 ILE B 191 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 1265 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 215 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO D 216 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 216 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 216 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 215 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO C 216 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 216 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 216 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 215 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.15e+00 pdb=" N PRO A 216 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " -0.029 5.00e-02 4.00e+02 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 841 2.75 - 3.29: 7691 3.29 - 3.82: 13489 3.82 - 4.36: 16014 4.36 - 4.90: 27417 Nonbonded interactions: 65452 Sorted by model distance: nonbonded pdb=" O CYS B 152 " pdb=" OG1 THR B 156 " model vdw 2.209 3.040 nonbonded pdb=" O CYS C 152 " pdb=" OG1 THR C 156 " model vdw 2.245 3.040 nonbonded pdb=" NZ LYS D 51 " pdb=" OD2 ASP B 185 " model vdw 2.272 3.120 nonbonded pdb=" O ASN A 49 " pdb=" OG SER A 53 " model vdw 2.294 3.040 nonbonded pdb=" OD1 ASN C 127 " pdb=" OG SER C 196 " model vdw 2.300 3.040 ... (remaining 65447 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 3 through 233 or resid 235 through 249)) selection = (chain 'B' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'C' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'D' and (resid 3 through 233 or resid 235 through 249)) } 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=0.48 max=1.00 mean=0.99 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: 2.000 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: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 25.330 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.004 0.033 7620 Z= 0.249 Angle : 0.611 8.785 10392 Z= 0.330 Chirality : 0.041 0.208 1268 Planarity : 0.005 0.054 1272 Dihedral : 12.297 89.556 2816 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.58 % Favored : 97.00 % Rotamer: Outliers : 2.03 % Allowed : 5.81 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.50 (0.26), residues: 980 helix: 1.64 (0.20), residues: 616 sheet: None (None), residues: 0 loop : -0.04 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 11 HIS 0.008 0.002 HIS D 180 PHE 0.013 0.002 PHE A 212 TYR 0.010 0.002 TYR A 227 ARG 0.002 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.817 Fit side-chains REVERT: D 123 SER cc_start: 0.8361 (p) cc_final: 0.8117 (t) REVERT: B 172 ILE cc_start: 0.8790 (mm) cc_final: 0.8435 (mt) REVERT: C 95 LEU cc_start: 0.8483 (tp) cc_final: 0.8039 (mp) REVERT: A 123 SER cc_start: 0.7644 (p) cc_final: 0.7411 (m) REVERT: A 159 ARG cc_start: 0.6977 (mtm180) cc_final: 0.6694 (mtm180) outliers start: 15 outliers final: 6 residues processed: 112 average time/residue: 0.1482 time to fit residues: 24.6321 Evaluate side-chains 99 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 191 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 ASN A 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7620 Z= 0.267 Angle : 0.585 8.635 10392 Z= 0.302 Chirality : 0.041 0.200 1268 Planarity : 0.005 0.051 1272 Dihedral : 8.495 59.288 1380 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.79 % Favored : 96.80 % Rotamer: Outliers : 1.76 % Allowed : 7.97 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.71 (0.28), residues: 980 helix: 1.80 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.07 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 11 HIS 0.007 0.001 HIS A 180 PHE 0.016 0.002 PHE A 212 TYR 0.010 0.002 TYR A 227 ARG 0.003 0.000 ARG C 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.780 Fit side-chains REVERT: D 123 SER cc_start: 0.8352 (p) cc_final: 0.8108 (t) REVERT: D 191 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8453 (mp) REVERT: B 172 ILE cc_start: 0.8789 (mm) cc_final: 0.8509 (mt) REVERT: C 95 LEU cc_start: 0.8486 (tp) cc_final: 0.8014 (mp) REVERT: A 123 SER cc_start: 0.7625 (p) cc_final: 0.7340 (m) outliers start: 13 outliers final: 9 residues processed: 102 average time/residue: 0.1520 time to fit residues: 22.8558 Evaluate side-chains 104 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7620 Z= 0.244 Angle : 0.561 8.408 10392 Z= 0.291 Chirality : 0.040 0.199 1268 Planarity : 0.005 0.050 1272 Dihedral : 8.114 59.795 1375 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.79 % Favored : 96.80 % Rotamer: Outliers : 1.89 % Allowed : 8.78 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.86 (0.28), residues: 980 helix: 1.94 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.07 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 11 HIS 0.006 0.001 HIS A 180 PHE 0.016 0.001 PHE A 212 TYR 0.011 0.001 TYR A 227 ARG 0.004 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.656 Fit side-chains REVERT: D 128 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8256 (m-30) REVERT: D 191 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8442 (mp) REVERT: B 172 ILE cc_start: 0.8801 (mm) cc_final: 0.8495 (mt) REVERT: C 95 LEU cc_start: 0.8455 (tp) cc_final: 0.8014 (mp) REVERT: A 123 SER cc_start: 0.7587 (p) cc_final: 0.7313 (m) outliers start: 14 outliers final: 6 residues processed: 100 average time/residue: 0.1381 time to fit residues: 21.0592 Evaluate side-chains 100 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 ASN A 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7620 Z= 0.178 Angle : 0.520 8.106 10392 Z= 0.270 Chirality : 0.039 0.193 1268 Planarity : 0.004 0.048 1272 Dihedral : 7.591 59.804 1374 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.79 % Favored : 96.80 % Rotamer: Outliers : 1.49 % Allowed : 8.78 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.05 (0.28), residues: 980 helix: 2.18 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -0.25 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 11 HIS 0.006 0.001 HIS A 180 PHE 0.014 0.001 PHE A 212 TYR 0.007 0.001 TYR A 227 ARG 0.003 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.743 Fit side-chains REVERT: D 191 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8042 (mp) REVERT: B 91 ILE cc_start: 0.8400 (mt) cc_final: 0.7977 (tt) REVERT: B 172 ILE cc_start: 0.8772 (mm) cc_final: 0.8428 (mt) REVERT: C 95 LEU cc_start: 0.8409 (tp) cc_final: 0.7979 (mp) REVERT: A 123 SER cc_start: 0.7552 (p) cc_final: 0.7294 (m) outliers start: 11 outliers final: 8 residues processed: 97 average time/residue: 0.1472 time to fit residues: 21.4270 Evaluate side-chains 94 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7620 Z= 0.199 Angle : 0.527 8.267 10392 Z= 0.274 Chirality : 0.039 0.196 1268 Planarity : 0.004 0.048 1272 Dihedral : 7.565 59.930 1374 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.00 % Favored : 96.59 % Rotamer: Outliers : 2.16 % Allowed : 8.11 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.09 (0.28), residues: 980 helix: 2.22 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -0.25 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 11 HIS 0.006 0.001 HIS A 180 PHE 0.014 0.001 PHE A 212 TYR 0.009 0.001 TYR A 227 ARG 0.004 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.679 Fit side-chains REVERT: D 191 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8069 (mp) REVERT: B 91 ILE cc_start: 0.8391 (mt) cc_final: 0.7976 (tt) REVERT: B 172 ILE cc_start: 0.8768 (mm) cc_final: 0.8428 (mt) REVERT: C 95 LEU cc_start: 0.8423 (tp) cc_final: 0.7983 (mp) REVERT: A 123 SER cc_start: 0.7575 (p) cc_final: 0.7314 (m) outliers start: 16 outliers final: 11 residues processed: 95 average time/residue: 0.1382 time to fit residues: 19.9907 Evaluate side-chains 97 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 92 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7620 Z= 0.171 Angle : 0.517 8.883 10392 Z= 0.266 Chirality : 0.038 0.190 1268 Planarity : 0.004 0.047 1272 Dihedral : 7.260 58.691 1374 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.89 % Favored : 96.69 % Rotamer: Outliers : 1.89 % Allowed : 7.97 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.26 (0.28), residues: 980 helix: 2.35 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -0.19 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 11 HIS 0.005 0.001 HIS D 180 PHE 0.014 0.001 PHE A 212 TYR 0.008 0.001 TYR A 227 ARG 0.003 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.777 Fit side-chains REVERT: D 191 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7933 (mp) REVERT: B 91 ILE cc_start: 0.8388 (mt) cc_final: 0.7983 (tt) REVERT: C 95 LEU cc_start: 0.8397 (tp) cc_final: 0.8057 (mp) REVERT: A 123 SER cc_start: 0.7549 (p) cc_final: 0.7288 (m) outliers start: 14 outliers final: 11 residues processed: 94 average time/residue: 0.1485 time to fit residues: 21.7712 Evaluate side-chains 99 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 0.041 7620 Z= 0.221 Angle : 0.547 8.280 10392 Z= 0.284 Chirality : 0.040 0.196 1268 Planarity : 0.004 0.047 1272 Dihedral : 7.516 59.739 1374 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.89 % Favored : 96.69 % Rotamer: Outliers : 1.89 % Allowed : 8.24 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.09 (0.28), residues: 980 helix: 2.23 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -0.26 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 11 HIS 0.006 0.001 HIS A 180 PHE 0.015 0.001 PHE A 212 TYR 0.010 0.001 TYR A 227 ARG 0.003 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.729 Fit side-chains REVERT: D 191 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8096 (mp) REVERT: B 91 ILE cc_start: 0.8397 (mt) cc_final: 0.7970 (tt) REVERT: B 172 ILE cc_start: 0.8775 (mm) cc_final: 0.8444 (mt) REVERT: C 95 LEU cc_start: 0.8444 (tp) cc_final: 0.7997 (mp) REVERT: A 123 SER cc_start: 0.7581 (p) cc_final: 0.7321 (m) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.1478 time to fit residues: 21.5195 Evaluate side-chains 102 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7620 Z= 0.268 Angle : 0.573 8.485 10392 Z= 0.297 Chirality : 0.041 0.201 1268 Planarity : 0.004 0.048 1272 Dihedral : 7.844 59.301 1374 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.79 % Favored : 96.80 % Rotamer: Outliers : 1.76 % Allowed : 8.51 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.90 (0.28), residues: 980 helix: 2.08 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -0.34 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 11 HIS 0.007 0.001 HIS A 180 PHE 0.017 0.002 PHE A 212 TYR 0.012 0.001 TYR A 227 ARG 0.003 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.756 Fit side-chains REVERT: B 172 ILE cc_start: 0.8802 (mm) cc_final: 0.8492 (mt) REVERT: C 95 LEU cc_start: 0.8475 (tp) cc_final: 0.8016 (mp) REVERT: A 123 SER cc_start: 0.7586 (p) cc_final: 0.7319 (m) outliers start: 13 outliers final: 11 residues processed: 93 average time/residue: 0.1411 time to fit residues: 19.9279 Evaluate side-chains 99 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7620 Z= 0.155 Angle : 0.513 8.128 10392 Z= 0.266 Chirality : 0.038 0.187 1268 Planarity : 0.004 0.047 1272 Dihedral : 7.187 58.685 1372 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.79 % Favored : 96.80 % Rotamer: Outliers : 1.35 % Allowed : 8.92 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.29 (0.28), residues: 980 helix: 2.45 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.32 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 11 HIS 0.005 0.001 HIS A 180 PHE 0.013 0.001 PHE A 212 TYR 0.007 0.001 TYR B 227 ARG 0.003 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.682 Fit side-chains REVERT: B 91 ILE cc_start: 0.8384 (mt) cc_final: 0.7967 (tt) REVERT: C 95 LEU cc_start: 0.8396 (tp) cc_final: 0.8007 (mp) REVERT: A 123 SER cc_start: 0.7542 (p) cc_final: 0.7285 (m) outliers start: 10 outliers final: 8 residues processed: 92 average time/residue: 0.1391 time to fit residues: 19.5130 Evaluate side-chains 93 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 88 optimal weight: 0.0030 chunk 76 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7620 Z= 0.205 Angle : 0.544 8.132 10392 Z= 0.283 Chirality : 0.039 0.193 1268 Planarity : 0.004 0.047 1272 Dihedral : 7.389 59.533 1372 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.89 % Favored : 96.69 % Rotamer: Outliers : 1.22 % Allowed : 9.32 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.19 (0.28), residues: 980 helix: 2.32 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -0.28 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 11 HIS 0.006 0.001 HIS A 180 PHE 0.015 0.001 PHE A 212 TYR 0.010 0.001 TYR A 227 ARG 0.003 0.000 ARG C 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 1.272 Fit side-chains REVERT: B 91 ILE cc_start: 0.8393 (mt) cc_final: 0.7972 (tt) REVERT: B 172 ILE cc_start: 0.8771 (mm) cc_final: 0.8427 (mt) REVERT: C 95 LEU cc_start: 0.8430 (tp) cc_final: 0.7985 (mp) REVERT: A 123 SER cc_start: 0.7581 (p) cc_final: 0.7319 (m) outliers start: 9 outliers final: 8 residues processed: 91 average time/residue: 0.1415 time to fit residues: 19.5747 Evaluate side-chains 94 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.131228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.105723 restraints weight = 30205.947| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.99 r_work: 0.2873 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7620 Z= 0.192 Angle : 0.536 8.124 10392 Z= 0.278 Chirality : 0.039 0.191 1268 Planarity : 0.004 0.047 1272 Dihedral : 7.325 58.880 1372 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.00 % Favored : 96.59 % Rotamer: Outliers : 1.22 % Allowed : 9.19 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.21 (0.28), residues: 980 helix: 2.34 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -0.28 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 11 HIS 0.006 0.001 HIS A 180 PHE 0.015 0.001 PHE A 212 TYR 0.009 0.001 TYR A 227 ARG 0.002 0.000 ARG C 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1937.13 seconds wall clock time: 36 minutes 2.10 seconds (2162.10 seconds total)