Starting phenix.real_space_refine on Tue Mar 3 17:35:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zcz_74046/03_2026/9zcz_74046.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zcz_74046/03_2026/9zcz_74046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zcz_74046/03_2026/9zcz_74046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zcz_74046/03_2026/9zcz_74046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zcz_74046/03_2026/9zcz_74046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zcz_74046/03_2026/9zcz_74046.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7464 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 1821 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1810 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 247, 1810 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1833 Chain: "B" Number of atoms: 1821 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1810 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 247, 1810 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1833 Chain: "C" Number of atoms: 1821 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1810 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 247, 1810 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1833 Chain: "A" Number of atoms: 1821 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1810 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 247, 1810 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1833 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 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: 3.13, per 1000 atoms: 0.42 Number of scatterers: 7464 At special positions: 0 Unit cell: (85.799, 85.799, 70.805, 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 468.9 milliseconds 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 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: 0.12 Creating SS restraints... Processing helix chain 'D' and resid 3 through 6 Processing helix chain 'D' and resid 7 through 33 removed outlier: 3.508A 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: 5.737A pdb=" N HIS D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 5.815A 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: 5.628A pdb=" N ASP D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 204 removed outlier: 3.699A 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: 3.612A pdb=" N LYS D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL D 244 " --> pdb=" O ASP D 240 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TRP D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 6 Processing helix chain 'B' and resid 7 through 33 removed outlier: 3.508A 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: 5.686A pdb=" N HIS B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 5.797A 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: 5.611A pdb=" N ASP B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 204 removed outlier: 3.694A 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: 3.610A pdb=" N LYS B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TRP B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 6 Processing helix chain 'C' and resid 7 through 33 removed outlier: 3.514A 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: 5.736A pdb=" N HIS C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 5.800A 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: 5.632A pdb=" N ASP C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 204 removed outlier: 3.706A 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: 3.626A pdb=" N LYS C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL C 244 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TRP C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) removed outlier: 4.179A 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: 3.509A 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: 5.726A pdb=" N HIS A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 5.800A 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: 5.619A pdb=" N ASP A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 204 removed outlier: 3.690A 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: 3.611A pdb=" N LYS A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TRP A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1596 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: 0.96 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2378 1.34 - 1.46: 1551 1.46 - 1.58: 3663 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 7616 Sorted by residual: bond pdb=" C1 PLM A 302 " pdb=" C2 PLM A 302 " ideal model delta sigma weight residual 1.542 1.499 0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" C1 PLM B 302 " pdb=" C2 PLM B 302 " ideal model delta sigma weight residual 1.542 1.499 0.043 2.00e-02 2.50e+03 4.63e+00 bond pdb=" C1 PLM C 302 " pdb=" C2 PLM C 302 " ideal model delta sigma weight residual 1.542 1.499 0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" C1 PLM D 302 " pdb=" C2 PLM D 302 " ideal model delta sigma weight residual 1.542 1.500 0.042 2.00e-02 2.50e+03 4.48e+00 bond pdb=" CA CYS C 189 " pdb=" C CYS C 189 " ideal model delta sigma weight residual 1.532 1.520 0.012 9.60e-03 1.09e+04 1.68e+00 ... (remaining 7611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 10049 1.47 - 2.93: 247 2.93 - 4.40: 62 4.40 - 5.87: 16 5.87 - 7.34: 6 Bond angle restraints: 10380 Sorted by residual: angle pdb=" N CYS A 87 " pdb=" CA CYS A 87 " pdb=" C CYS A 87 " ideal model delta sigma weight residual 111.24 115.93 -4.69 1.38e+00 5.25e-01 1.16e+01 angle pdb=" N CYS B 87 " pdb=" CA CYS B 87 " pdb=" C CYS B 87 " ideal model delta sigma weight residual 111.24 115.83 -4.59 1.38e+00 5.25e-01 1.11e+01 angle pdb=" N CYS C 87 " pdb=" CA CYS C 87 " pdb=" C CYS C 87 " ideal model delta sigma weight residual 111.24 115.79 -4.55 1.38e+00 5.25e-01 1.09e+01 angle pdb=" N CYS D 87 " pdb=" CA CYS D 87 " pdb=" C CYS D 87 " ideal model delta sigma weight residual 111.24 115.65 -4.41 1.38e+00 5.25e-01 1.02e+01 angle pdb=" CA CYS D 189 " pdb=" CB CYS D 189 " pdb=" SG CYS D 189 " ideal model delta sigma weight residual 114.40 107.06 7.34 2.30e+00 1.89e-01 1.02e+01 ... (remaining 10375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4109 17.97 - 35.93: 364 35.93 - 53.90: 83 53.90 - 71.87: 12 71.87 - 89.83: 12 Dihedral angle restraints: 4580 sinusoidal: 1804 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 -157.22 -22.78 0 5.00e+00 4.00e-02 2.08e+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 -157.55 -22.45 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU C 182 " pdb=" C LEU C 182 " pdb=" N ALA C 183 " pdb=" CA ALA C 183 " ideal model delta harmonic sigma weight residual 180.00 -157.86 -22.14 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 4577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 847 0.032 - 0.064: 318 0.064 - 0.096: 77 0.096 - 0.129: 21 0.129 - 0.161: 5 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CA CYS A 87 " pdb=" N CYS A 87 " pdb=" C CYS A 87 " pdb=" CB CYS A 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CA CYS C 87 " pdb=" N CYS C 87 " pdb=" C CYS C 87 " pdb=" CB CYS C 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA CYS D 87 " pdb=" N CYS D 87 " pdb=" C CYS D 87 " pdb=" CB CYS D 87 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 1265 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 191 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C ILE A 191 " 0.020 2.00e-02 2.50e+03 pdb=" O ILE A 191 " -0.008 2.00e-02 2.50e+03 pdb=" N ASN A 192 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 76 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO B 77 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 77 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 77 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 225 " 0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C LEU C 225 " -0.020 2.00e-02 2.50e+03 pdb=" O LEU C 225 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE C 226 " 0.007 2.00e-02 2.50e+03 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 4036 2.98 - 3.46: 8477 3.46 - 3.94: 13602 3.94 - 4.42: 15703 4.42 - 4.90: 24437 Nonbonded interactions: 66255 Sorted by model distance: nonbonded pdb=" OH TYR D 186 " pdb=" O GLY C 30 " model vdw 2.499 3.040 nonbonded pdb=" OH TYR C 186 " pdb=" O GLY A 30 " model vdw 2.501 3.040 nonbonded pdb=" O GLY D 30 " pdb=" OH TYR B 186 " model vdw 2.509 3.040 nonbonded pdb=" O GLY B 30 " pdb=" OH TYR A 186 " model vdw 2.511 3.040 nonbonded pdb=" NZ LYS B 51 " pdb=" OD2 ASP A 185 " model vdw 2.511 3.120 ... (remaining 66250 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: 0.03 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'B' selection = chain 'C' selection = chain 'A' } 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: 1.690 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.550 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 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 0.043 7620 Z= 0.197 Angle : 0.634 7.337 10380 Z= 0.347 Chirality : 0.038 0.161 1268 Planarity : 0.003 0.029 1272 Dihedral : 14.867 89.834 2812 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.96 % Favored : 96.63 % Rotamer: Outliers : 0.67 % Allowed : 14.78 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.26), residues: 992 helix: 1.76 (0.19), residues: 652 sheet: None (None), residues: 0 loop : -0.31 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.010 0.002 TYR D 227 PHE 0.018 0.002 PHE A 212 TRP 0.004 0.001 TRP C 11 HIS 0.004 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 7616) covalent geometry : angle 0.63401 (10380) hydrogen bonds : bond 0.09905 ( 540) hydrogen bonds : angle 6.24304 ( 1596) Misc. bond : bond 0.03732 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.266 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 120 average time/residue: 0.5588 time to fit residues: 70.6872 Evaluate side-chains 93 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.083878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.067044 restraints weight = 51298.608| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.31 r_work: 0.2645 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7620 Z= 0.130 Angle : 0.536 7.677 10380 Z= 0.282 Chirality : 0.040 0.231 1268 Planarity : 0.004 0.030 1272 Dihedral : 7.390 59.415 1364 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.04 % Favored : 97.55 % Rotamer: Outliers : 2.15 % Allowed : 11.29 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.28), residues: 992 helix: 2.45 (0.19), residues: 656 sheet: None (None), residues: 0 loop : 0.32 (0.39), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 159 TYR 0.006 0.001 TYR C 97 PHE 0.014 0.001 PHE B 212 TRP 0.008 0.001 TRP C 11 HIS 0.005 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7616) covalent geometry : angle 0.53559 (10380) hydrogen bonds : bond 0.04121 ( 540) hydrogen bonds : angle 5.21046 ( 1596) Misc. bond : bond 0.00090 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.279 Fit side-chains REVERT: C 185 ASP cc_start: 0.8941 (m-30) cc_final: 0.8701 (m-30) REVERT: A 185 ASP cc_start: 0.8970 (m-30) cc_final: 0.8677 (m-30) outliers start: 16 outliers final: 2 residues processed: 104 average time/residue: 0.6050 time to fit residues: 66.1692 Evaluate side-chains 84 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 191 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 GLN C 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.083961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.067450 restraints weight = 45568.749| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.19 r_work: 0.2656 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7620 Z= 0.121 Angle : 0.503 6.981 10380 Z= 0.267 Chirality : 0.039 0.188 1268 Planarity : 0.003 0.034 1272 Dihedral : 6.805 52.985 1364 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.14 % Favored : 97.45 % Rotamer: Outliers : 1.21 % Allowed : 11.83 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.28), residues: 992 helix: 2.63 (0.19), residues: 656 sheet: None (None), residues: 0 loop : 0.39 (0.41), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 159 TYR 0.006 0.001 TYR A 227 PHE 0.014 0.001 PHE A 212 TRP 0.008 0.001 TRP A 11 HIS 0.005 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 7616) covalent geometry : angle 0.50330 (10380) hydrogen bonds : bond 0.04045 ( 540) hydrogen bonds : angle 5.09909 ( 1596) Misc. bond : bond 0.00037 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.242 Fit side-chains REVERT: D 8 LYS cc_start: 0.7772 (mptt) cc_final: 0.7322 (mtmm) REVERT: D 185 ASP cc_start: 0.8953 (m-30) cc_final: 0.8648 (m-30) REVERT: B 8 LYS cc_start: 0.7849 (mptt) cc_final: 0.7411 (mtmm) REVERT: B 185 ASP cc_start: 0.8943 (m-30) cc_final: 0.8665 (m-30) REVERT: C 185 ASP cc_start: 0.8940 (m-30) cc_final: 0.8693 (m-30) REVERT: A 185 ASP cc_start: 0.8910 (m-30) cc_final: 0.8662 (m-30) outliers start: 9 outliers final: 5 residues processed: 94 average time/residue: 0.6421 time to fit residues: 63.3809 Evaluate side-chains 79 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain A residue 115 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.083615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.066933 restraints weight = 51793.638| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.32 r_work: 0.2641 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7620 Z= 0.122 Angle : 0.498 7.038 10380 Z= 0.264 Chirality : 0.039 0.169 1268 Planarity : 0.003 0.037 1272 Dihedral : 6.802 53.089 1364 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.14 % Favored : 97.45 % Rotamer: Outliers : 0.94 % Allowed : 10.48 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.28), residues: 992 helix: 2.64 (0.20), residues: 656 sheet: None (None), residues: 0 loop : 0.36 (0.40), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 241 TYR 0.006 0.001 TYR D 227 PHE 0.013 0.001 PHE B 212 TRP 0.008 0.001 TRP A 11 HIS 0.005 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7616) covalent geometry : angle 0.49847 (10380) hydrogen bonds : bond 0.04017 ( 540) hydrogen bonds : angle 5.06129 ( 1596) Misc. bond : bond 0.00033 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.283 Fit side-chains REVERT: D 8 LYS cc_start: 0.7737 (mptt) cc_final: 0.7298 (mtmm) REVERT: D 185 ASP cc_start: 0.8945 (m-30) cc_final: 0.8630 (m-30) REVERT: B 8 LYS cc_start: 0.7725 (mptt) cc_final: 0.7276 (mtmm) REVERT: B 51 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8379 (tttt) REVERT: B 185 ASP cc_start: 0.8958 (m-30) cc_final: 0.8696 (m-30) REVERT: C 8 LYS cc_start: 0.7826 (mptt) cc_final: 0.7389 (mtmm) REVERT: C 185 ASP cc_start: 0.8944 (m-30) cc_final: 0.8680 (m-30) REVERT: A 8 LYS cc_start: 0.7727 (mptt) cc_final: 0.7284 (mtmm) outliers start: 7 outliers final: 4 residues processed: 94 average time/residue: 0.6811 time to fit residues: 66.9910 Evaluate side-chains 88 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain A residue 115 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.081681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.065245 restraints weight = 39739.871| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.02 r_work: 0.2621 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2516 r_free = 0.2516 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2516 r_free = 0.2516 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7620 Z= 0.142 Angle : 0.514 7.265 10380 Z= 0.272 Chirality : 0.040 0.174 1268 Planarity : 0.004 0.040 1272 Dihedral : 7.209 53.512 1364 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.24 % Favored : 97.35 % Rotamer: Outliers : 0.94 % Allowed : 11.56 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.28), residues: 992 helix: 2.59 (0.20), residues: 656 sheet: None (None), residues: 0 loop : 0.40 (0.41), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 241 TYR 0.007 0.001 TYR D 227 PHE 0.014 0.001 PHE B 212 TRP 0.008 0.001 TRP A 11 HIS 0.005 0.002 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7616) covalent geometry : angle 0.51449 (10380) hydrogen bonds : bond 0.04339 ( 540) hydrogen bonds : angle 5.12041 ( 1596) Misc. bond : bond 0.00048 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.244 Fit side-chains REVERT: D 8 LYS cc_start: 0.7727 (mptt) cc_final: 0.7282 (mtmm) REVERT: D 185 ASP cc_start: 0.9062 (m-30) cc_final: 0.8756 (m-30) REVERT: B 8 LYS cc_start: 0.7659 (mptt) cc_final: 0.7206 (mtmm) REVERT: B 51 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8390 (tttt) REVERT: B 185 ASP cc_start: 0.9060 (m-30) cc_final: 0.8796 (m-30) REVERT: C 8 LYS cc_start: 0.7659 (mptt) cc_final: 0.7209 (mtmm) REVERT: C 185 ASP cc_start: 0.9047 (m-30) cc_final: 0.8777 (m-30) REVERT: A 8 LYS cc_start: 0.7679 (mptt) cc_final: 0.7217 (mtmm) REVERT: A 185 ASP cc_start: 0.9064 (m-30) cc_final: 0.8446 (m-30) outliers start: 7 outliers final: 5 residues processed: 95 average time/residue: 0.6813 time to fit residues: 67.7174 Evaluate side-chains 90 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain A residue 115 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.079115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.062480 restraints weight = 43033.593| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 3.11 r_work: 0.2569 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2467 r_free = 0.2467 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2467 r_free = 0.2467 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9184 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 7620 Z= 0.212 Angle : 0.559 7.420 10380 Z= 0.295 Chirality : 0.042 0.185 1268 Planarity : 0.004 0.044 1272 Dihedral : 8.414 56.100 1364 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.35 % Favored : 97.24 % Rotamer: Outliers : 0.94 % Allowed : 11.42 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.29), residues: 992 helix: 2.44 (0.20), residues: 648 sheet: None (None), residues: 0 loop : 0.21 (0.41), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 241 TYR 0.009 0.002 TYR D 227 PHE 0.018 0.002 PHE B 212 TRP 0.007 0.001 TRP A 11 HIS 0.006 0.002 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 7616) covalent geometry : angle 0.55859 (10380) hydrogen bonds : bond 0.04952 ( 540) hydrogen bonds : angle 5.30502 ( 1596) Misc. bond : bond 0.00096 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.265 Fit side-chains REVERT: D 8 LYS cc_start: 0.7747 (mptt) cc_final: 0.7302 (mtmm) REVERT: D 185 ASP cc_start: 0.9100 (m-30) cc_final: 0.8817 (m-30) REVERT: B 8 LYS cc_start: 0.7747 (mptt) cc_final: 0.7299 (mtmm) REVERT: B 51 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8396 (tttt) REVERT: B 185 ASP cc_start: 0.9104 (m-30) cc_final: 0.8838 (m-30) REVERT: C 8 LYS cc_start: 0.7744 (mptt) cc_final: 0.7301 (mtmm) REVERT: C 185 ASP cc_start: 0.9091 (m-30) cc_final: 0.8811 (m-30) REVERT: A 185 ASP cc_start: 0.9099 (m-30) cc_final: 0.8543 (m-30) outliers start: 7 outliers final: 3 residues processed: 91 average time/residue: 0.7295 time to fit residues: 69.2071 Evaluate side-chains 88 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain A residue 115 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.081294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.064457 restraints weight = 56066.987| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.40 r_work: 0.2598 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7620 Z= 0.144 Angle : 0.513 7.127 10380 Z= 0.271 Chirality : 0.039 0.174 1268 Planarity : 0.004 0.042 1272 Dihedral : 8.140 58.871 1364 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.04 % Favored : 97.55 % Rotamer: Outliers : 0.94 % Allowed : 11.83 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.29), residues: 992 helix: 2.54 (0.20), residues: 648 sheet: None (None), residues: 0 loop : 0.22 (0.41), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.007 0.001 TYR D 227 PHE 0.014 0.001 PHE D 212 TRP 0.008 0.001 TRP A 11 HIS 0.005 0.002 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7616) covalent geometry : angle 0.51299 (10380) hydrogen bonds : bond 0.04315 ( 540) hydrogen bonds : angle 5.16723 ( 1596) Misc. bond : bond 0.00051 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.227 Fit side-chains REVERT: D 8 LYS cc_start: 0.7670 (mptt) cc_final: 0.7225 (mtmm) REVERT: D 185 ASP cc_start: 0.8950 (m-30) cc_final: 0.8640 (m-30) REVERT: B 8 LYS cc_start: 0.7606 (mptt) cc_final: 0.7153 (mtmm) REVERT: B 51 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8313 (tttt) REVERT: B 185 ASP cc_start: 0.8956 (m-30) cc_final: 0.8681 (m-30) REVERT: C 8 LYS cc_start: 0.7669 (mptt) cc_final: 0.7226 (mtmm) REVERT: C 185 ASP cc_start: 0.8947 (m-30) cc_final: 0.8634 (m-30) REVERT: A 8 LYS cc_start: 0.7765 (mptt) cc_final: 0.7303 (mtmm) REVERT: A 185 ASP cc_start: 0.8954 (m-30) cc_final: 0.8331 (m-30) outliers start: 7 outliers final: 3 residues processed: 95 average time/residue: 0.6933 time to fit residues: 68.9286 Evaluate side-chains 89 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain A residue 115 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 0.0000 chunk 22 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.079884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.063142 restraints weight = 48519.554| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 3.25 r_work: 0.2580 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7620 Z= 0.182 Angle : 0.538 7.252 10380 Z= 0.284 Chirality : 0.041 0.180 1268 Planarity : 0.004 0.043 1272 Dihedral : 8.326 56.625 1364 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.35 % Favored : 97.24 % Rotamer: Outliers : 0.81 % Allowed : 11.83 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.29), residues: 992 helix: 2.45 (0.20), residues: 648 sheet: None (None), residues: 0 loop : 0.14 (0.41), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 241 TYR 0.008 0.001 TYR D 227 PHE 0.016 0.002 PHE D 212 TRP 0.007 0.001 TRP B 11 HIS 0.006 0.002 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 7616) covalent geometry : angle 0.53841 (10380) hydrogen bonds : bond 0.04708 ( 540) hydrogen bonds : angle 5.24172 ( 1596) Misc. bond : bond 0.00077 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.271 Fit side-chains REVERT: D 8 LYS cc_start: 0.7692 (mptt) cc_final: 0.7255 (mtmm) REVERT: D 185 ASP cc_start: 0.8977 (m-30) cc_final: 0.8689 (m-30) REVERT: B 8 LYS cc_start: 0.7692 (mptt) cc_final: 0.7256 (mtmm) REVERT: B 51 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8354 (tttt) REVERT: B 185 ASP cc_start: 0.8962 (m-30) cc_final: 0.8683 (m-30) REVERT: C 8 LYS cc_start: 0.7733 (mptt) cc_final: 0.7303 (mtmm) REVERT: C 185 ASP cc_start: 0.8965 (m-30) cc_final: 0.8677 (m-30) REVERT: A 8 LYS cc_start: 0.7800 (mptt) cc_final: 0.7342 (mtmm) REVERT: A 185 ASP cc_start: 0.8967 (m-30) cc_final: 0.8384 (m-30) outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.7541 time to fit residues: 70.0140 Evaluate side-chains 88 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain A residue 115 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.0060 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.0370 overall best weight: 0.4874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.084490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.068298 restraints weight = 41173.433| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.05 r_work: 0.2673 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7620 Z= 0.109 Angle : 0.486 6.687 10380 Z= 0.256 Chirality : 0.038 0.165 1268 Planarity : 0.003 0.039 1272 Dihedral : 7.675 58.513 1364 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.45 % Favored : 97.14 % Rotamer: Outliers : 0.81 % Allowed : 12.10 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.28), residues: 992 helix: 2.69 (0.20), residues: 648 sheet: None (None), residues: 0 loop : 0.13 (0.40), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 241 TYR 0.006 0.001 TYR D 227 PHE 0.011 0.001 PHE D 212 TRP 0.008 0.001 TRP C 11 HIS 0.005 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 7616) covalent geometry : angle 0.48616 (10380) hydrogen bonds : bond 0.03735 ( 540) hydrogen bonds : angle 5.04012 ( 1596) Misc. bond : bond 0.00020 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.277 Fit side-chains REVERT: D 8 LYS cc_start: 0.7655 (mptt) cc_final: 0.7200 (mtmm) REVERT: B 8 LYS cc_start: 0.7657 (mptt) cc_final: 0.7209 (mtmm) REVERT: B 185 ASP cc_start: 0.8922 (m-30) cc_final: 0.8637 (m-30) REVERT: C 8 LYS cc_start: 0.7664 (mptt) cc_final: 0.7210 (mtmm) REVERT: A 8 LYS cc_start: 0.7746 (mptt) cc_final: 0.7283 (mtmm) REVERT: A 185 ASP cc_start: 0.8911 (m-30) cc_final: 0.8601 (m-30) outliers start: 6 outliers final: 2 residues processed: 100 average time/residue: 0.6435 time to fit residues: 67.4011 Evaluate side-chains 96 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 191 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.083122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.066473 restraints weight = 52861.248| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.34 r_work: 0.2634 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7620 Z= 0.125 Angle : 0.496 6.892 10380 Z= 0.262 Chirality : 0.039 0.168 1268 Planarity : 0.004 0.041 1272 Dihedral : 7.666 58.091 1364 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.04 % Favored : 97.55 % Rotamer: Outliers : 0.54 % Allowed : 11.83 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.29), residues: 992 helix: 2.66 (0.20), residues: 656 sheet: None (None), residues: 0 loop : 0.28 (0.41), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 241 TYR 0.007 0.001 TYR D 227 PHE 0.012 0.001 PHE D 212 TRP 0.009 0.001 TRP D 11 HIS 0.005 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7616) covalent geometry : angle 0.49611 (10380) hydrogen bonds : bond 0.04029 ( 540) hydrogen bonds : angle 5.05082 ( 1596) Misc. bond : bond 0.00033 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.280 Fit side-chains REVERT: D 8 LYS cc_start: 0.7670 (mptt) cc_final: 0.7219 (mtmm) REVERT: D 185 ASP cc_start: 0.8939 (m-30) cc_final: 0.8628 (m-30) REVERT: B 8 LYS cc_start: 0.7631 (mptt) cc_final: 0.7186 (mtmm) REVERT: B 185 ASP cc_start: 0.8950 (m-30) cc_final: 0.8675 (m-30) REVERT: C 8 LYS cc_start: 0.7679 (mptt) cc_final: 0.7239 (mtmm) REVERT: C 185 ASP cc_start: 0.8929 (m-30) cc_final: 0.8603 (m-30) REVERT: A 8 LYS cc_start: 0.7738 (mptt) cc_final: 0.7277 (mtmm) REVERT: A 185 ASP cc_start: 0.8935 (m-30) cc_final: 0.8642 (m-30) outliers start: 4 outliers final: 4 residues processed: 93 average time/residue: 0.7268 time to fit residues: 70.6675 Evaluate side-chains 95 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain A residue 191 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 95 optimal weight: 0.0270 chunk 4 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.083635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.067148 restraints weight = 47305.663| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.22 r_work: 0.2647 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7620 Z= 0.119 Angle : 0.492 6.836 10380 Z= 0.260 Chirality : 0.038 0.166 1268 Planarity : 0.003 0.040 1272 Dihedral : 7.528 57.454 1364 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.14 % Favored : 97.45 % Rotamer: Outliers : 0.54 % Allowed : 11.83 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.29), residues: 992 helix: 2.68 (0.20), residues: 656 sheet: None (None), residues: 0 loop : 0.30 (0.41), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 241 TYR 0.007 0.001 TYR D 227 PHE 0.012 0.001 PHE A 212 TRP 0.009 0.001 TRP D 11 HIS 0.005 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7616) covalent geometry : angle 0.49159 (10380) hydrogen bonds : bond 0.03935 ( 540) hydrogen bonds : angle 5.03049 ( 1596) Misc. bond : bond 0.00029 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2564.22 seconds wall clock time: 44 minutes 22.09 seconds (2662.09 seconds total)