Starting phenix.real_space_refine on Sat Aug 23 01:38:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j0f_35901/08_2025/8j0f_35901.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j0f_35901/08_2025/8j0f_35901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j0f_35901/08_2025/8j0f_35901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j0f_35901/08_2025/8j0f_35901.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j0f_35901/08_2025/8j0f_35901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j0f_35901/08_2025/8j0f_35901.map" } resolution = 3.3 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= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 5588 2.51 5 N 1572 2.21 5 O 1720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8932 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2067 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 2 Chain: "F" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "A" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2067 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 2 Chain: "E" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "B" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2067 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 2 Chain: "G" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "D" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2067 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 2 Chain: "H" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 1.88, per 1000 atoms: 0.21 Number of scatterers: 8932 At special positions: 0 Unit cell: (102.82, 92.22, 94.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 12 15.00 Mg 4 11.99 O 1720 8.00 N 1572 7.00 C 5588 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: 0.59 Conformation dependent library (CDL) restraints added in 269.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB RGP C 802 " pdb=" CB RGP A 802 " pdb=" CB RGP B 802 " pdb=" CB RGP D 802 " Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 58.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'C' and resid 5 through 13 removed outlier: 5.346A pdb=" N PHE C 10 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 27 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.791A pdb=" N GLY C 31 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 51 Processing helix chain 'C' and resid 61 through 78 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 91 through 114 removed outlier: 3.705A pdb=" N SER C 101 " --> pdb=" O GLY C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.700A pdb=" N ARG C 129 " --> pdb=" O SER C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 147 Processing helix chain 'C' and resid 175 through 187 Processing helix chain 'C' and resid 237 through 253 removed outlier: 3.862A pdb=" N LYS C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 4.350A pdb=" N SER C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 286 removed outlier: 3.702A pdb=" N HIS C 285 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 77 Processing helix chain 'F' and resid 79 through 85 Processing helix chain 'A' and resid 5 through 13 removed outlier: 5.346A pdb=" N PHE A 10 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.791A pdb=" N GLY A 31 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 51 Processing helix chain 'A' and resid 61 through 78 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 91 through 114 removed outlier: 3.705A pdb=" N SER A 101 " --> pdb=" O GLY A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.700A pdb=" N ARG A 129 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 147 Processing helix chain 'A' and resid 175 through 187 Processing helix chain 'A' and resid 237 through 253 removed outlier: 3.862A pdb=" N LYS A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 4.350A pdb=" N SER A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.702A pdb=" N HIS A 285 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 Processing helix chain 'E' and resid 79 through 85 Processing helix chain 'B' and resid 5 through 13 removed outlier: 5.346A pdb=" N PHE B 10 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.791A pdb=" N GLY B 31 " --> pdb=" O GLY B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 51 Processing helix chain 'B' and resid 61 through 78 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 91 through 114 removed outlier: 3.705A pdb=" N SER B 101 " --> pdb=" O GLY B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.700A pdb=" N ARG B 129 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 Processing helix chain 'B' and resid 175 through 187 Processing helix chain 'B' and resid 237 through 253 removed outlier: 3.862A pdb=" N LYS B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 4.350A pdb=" N SER B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 286 removed outlier: 3.702A pdb=" N HIS B 285 " --> pdb=" O GLN B 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 77 Processing helix chain 'G' and resid 79 through 85 Processing helix chain 'D' and resid 5 through 13 removed outlier: 5.346A pdb=" N PHE D 10 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.791A pdb=" N GLY D 31 " --> pdb=" O GLY D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 51 Processing helix chain 'D' and resid 61 through 78 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 91 through 114 removed outlier: 3.705A pdb=" N SER D 101 " --> pdb=" O GLY D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.700A pdb=" N ARG D 129 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 147 Processing helix chain 'D' and resid 175 through 187 Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.862A pdb=" N LYS D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 removed outlier: 4.350A pdb=" N SER D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 286 removed outlier: 3.702A pdb=" N HIS D 285 " --> pdb=" O GLN D 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 Processing helix chain 'H' and resid 79 through 85 Processing sheet with id=AA1, first strand: chain 'C' and resid 117 through 123 removed outlier: 7.008A pdb=" N THR C 117 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL C 152 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA C 119 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN C 154 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET C 121 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL C 55 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG C 16 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE C 193 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL C 18 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU C 195 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS C 20 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C 192 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR C 259 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU C 194 " --> pdb=" O THR C 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 117 through 123 removed outlier: 7.008A pdb=" N THR A 117 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL A 152 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA A 119 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN A 154 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET A 121 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL A 55 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG A 16 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE A 193 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 18 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU A 195 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS A 20 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 192 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR A 259 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU A 194 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 123 removed outlier: 7.008A pdb=" N THR B 117 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL B 152 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA B 119 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN B 154 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET B 121 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL B 55 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG B 16 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE B 193 " --> pdb=" O ARG B 16 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 18 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU B 195 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS B 20 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU B 192 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR B 259 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU B 194 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 117 through 123 removed outlier: 7.008A pdb=" N THR D 117 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL D 152 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA D 119 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN D 154 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET D 121 " --> pdb=" O ASN D 154 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL D 55 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG D 16 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE D 193 " --> pdb=" O ARG D 16 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL D 18 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU D 195 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS D 20 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU D 192 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR D 259 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU D 194 " --> pdb=" O THR D 259 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1212 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: 0.92 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1788 1.32 - 1.44: 2040 1.44 - 1.56: 5136 1.56 - 1.68: 20 1.68 - 1.80: 64 Bond restraints: 9048 Sorted by residual: bond pdb=" OE2 RGP D 802 " pdb=" PA RGP D 802 " ideal model delta sigma weight residual 1.798 1.608 0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" OE2 RGP C 802 " pdb=" PA RGP C 802 " ideal model delta sigma weight residual 1.798 1.608 0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" OE2 RGP A 802 " pdb=" PA RGP A 802 " ideal model delta sigma weight residual 1.798 1.608 0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" OE2 RGP B 802 " pdb=" PA RGP B 802 " ideal model delta sigma weight residual 1.798 1.608 0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" CD RGP A 802 " pdb=" OE2 RGP A 802 " ideal model delta sigma weight residual 1.302 1.455 -0.153 2.00e-02 2.50e+03 5.86e+01 ... (remaining 9043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 11268 1.67 - 3.34: 620 3.34 - 5.01: 224 5.01 - 6.68: 80 6.68 - 8.34: 20 Bond angle restraints: 12212 Sorted by residual: angle pdb=" N ILE C 150 " pdb=" CA ILE C 150 " pdb=" C ILE C 150 " ideal model delta sigma weight residual 107.56 112.87 -5.31 9.10e-01 1.21e+00 3.40e+01 angle pdb=" N ILE B 150 " pdb=" CA ILE B 150 " pdb=" C ILE B 150 " ideal model delta sigma weight residual 107.56 112.87 -5.31 9.10e-01 1.21e+00 3.40e+01 angle pdb=" N ILE D 150 " pdb=" CA ILE D 150 " pdb=" C ILE D 150 " ideal model delta sigma weight residual 107.56 112.87 -5.31 9.10e-01 1.21e+00 3.40e+01 angle pdb=" N ILE A 150 " pdb=" CA ILE A 150 " pdb=" C ILE A 150 " ideal model delta sigma weight residual 107.56 112.87 -5.31 9.10e-01 1.21e+00 3.40e+01 angle pdb=" N VAL B 254 " pdb=" CA VAL B 254 " pdb=" C VAL B 254 " ideal model delta sigma weight residual 107.55 112.76 -5.21 9.90e-01 1.02e+00 2.77e+01 ... (remaining 12207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.62: 5260 34.62 - 69.24: 178 69.24 - 103.86: 16 103.86 - 138.48: 8 138.48 - 173.11: 2 Dihedral angle restraints: 5464 sinusoidal: 2216 harmonic: 3248 Sorted by residual: dihedral pdb=" O1B ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 113.10 -173.11 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP C 801 " pdb=" O3A ADP C 801 " pdb=" PB ADP C 801 " pdb=" PA ADP C 801 " ideal model delta sinusoidal sigma weight residual -60.00 113.10 -173.11 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP D 801 " pdb=" O5' ADP D 801 " pdb=" PA ADP D 801 " pdb=" O2A ADP D 801 " ideal model delta sinusoidal sigma weight residual 300.00 170.94 129.07 1 2.00e+01 2.50e-03 3.91e+01 ... (remaining 5461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 972 0.043 - 0.085: 320 0.085 - 0.128: 96 0.128 - 0.170: 8 0.170 - 0.213: 12 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA MET D 110 " pdb=" N MET D 110 " pdb=" C MET D 110 " pdb=" CB MET D 110 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA MET C 110 " pdb=" N MET C 110 " pdb=" C MET C 110 " pdb=" CB MET C 110 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA MET B 110 " pdb=" N MET B 110 " pdb=" C MET B 110 " pdb=" CB MET B 110 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1405 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 115 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" CG ASP A 115 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP A 115 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A 115 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 115 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" CG ASP C 115 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP C 115 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP C 115 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 115 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" CG ASP D 115 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP D 115 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP D 115 " 0.013 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2014 2.77 - 3.31: 9110 3.31 - 3.84: 14972 3.84 - 4.37: 17476 4.37 - 4.90: 28944 Nonbonded interactions: 72516 Sorted by model distance: nonbonded pdb=" N GLU D 265 " pdb=" OE1 GLU D 265 " model vdw 2.242 3.120 nonbonded pdb=" N GLU B 265 " pdb=" OE1 GLU B 265 " model vdw 2.242 3.120 nonbonded pdb=" N GLU A 265 " pdb=" OE1 GLU A 265 " model vdw 2.242 3.120 nonbonded pdb=" N GLU C 265 " pdb=" OE1 GLU C 265 " model vdw 2.242 3.120 nonbonded pdb=" OD2 ASP B 208 " pdb=" OG1 THR B 210 " model vdw 2.246 3.040 ... (remaining 72511 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: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'E' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.460 Find NCS groups from input model: 0.050 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.009 0.190 9048 Z= 0.588 Angle : 1.064 8.344 12212 Z= 0.653 Chirality : 0.047 0.213 1408 Planarity : 0.005 0.047 1544 Dihedral : 18.094 173.106 3368 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.13 % Allowed : 20.43 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.30 (0.27), residues: 1108 helix: 0.35 (0.22), residues: 580 sheet: -0.20 (0.41), residues: 188 loop : 0.56 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 134 TYR 0.024 0.002 TYR D 106 PHE 0.019 0.001 PHE B 153 TRP 0.005 0.001 TRP C 174 HIS 0.006 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00925 ( 9048) covalent geometry : angle 1.06430 (12212) hydrogen bonds : bond 0.18839 ( 460) hydrogen bonds : angle 5.98584 ( 1212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.245 Fit side-chains REVERT: C 68 GLN cc_start: 0.8657 (tm-30) cc_final: 0.7830 (tm-30) REVERT: A 68 GLN cc_start: 0.8651 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 68 GLN cc_start: 0.8641 (tm-30) cc_final: 0.7797 (tm-30) REVERT: D 68 GLN cc_start: 0.8648 (tm-30) cc_final: 0.7791 (tm-30) outliers start: 20 outliers final: 0 residues processed: 194 average time/residue: 0.0824 time to fit residues: 21.6418 Evaluate side-chains 179 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.091812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.071752 restraints weight = 21907.257| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 4.09 r_work: 0.2928 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9048 Z= 0.134 Angle : 0.677 9.136 12212 Z= 0.328 Chirality : 0.041 0.132 1408 Planarity : 0.003 0.022 1544 Dihedral : 13.523 179.208 1300 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.28 % Allowed : 18.94 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.12 (0.26), residues: 1108 helix: 1.08 (0.21), residues: 596 sheet: 0.02 (0.41), residues: 188 loop : 0.89 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 67 TYR 0.022 0.002 TYR B 106 PHE 0.025 0.002 PHE F 80 TRP 0.003 0.000 TRP D 287 HIS 0.002 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9048) covalent geometry : angle 0.67686 (12212) hydrogen bonds : bond 0.04578 ( 460) hydrogen bonds : angle 3.93215 ( 1212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.340 Fit side-chains REVERT: C 80 PHE cc_start: 0.9388 (t80) cc_final: 0.9165 (t80) REVERT: C 115 ASP cc_start: 0.8941 (t0) cc_final: 0.8740 (t0) REVERT: C 186 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8334 (tm-30) REVERT: C 228 PHE cc_start: 0.8268 (m-10) cc_final: 0.8043 (m-10) REVERT: A 89 GLU cc_start: 0.8718 (tp30) cc_final: 0.8516 (tp30) REVERT: A 115 ASP cc_start: 0.8940 (t0) cc_final: 0.8736 (t0) REVERT: A 131 LYS cc_start: 0.9236 (pttm) cc_final: 0.8962 (mmmt) REVERT: A 228 PHE cc_start: 0.8287 (m-10) cc_final: 0.8051 (m-10) REVERT: B 54 GLU cc_start: 0.8700 (mp0) cc_final: 0.8050 (pm20) REVERT: B 115 ASP cc_start: 0.8951 (t0) cc_final: 0.8742 (t0) REVERT: B 132 ASP cc_start: 0.8865 (t0) cc_final: 0.8592 (t0) REVERT: B 220 GLU cc_start: 0.9486 (tp30) cc_final: 0.9162 (tm-30) REVERT: B 251 TYR cc_start: 0.8649 (m-80) cc_final: 0.8316 (m-80) REVERT: D 115 ASP cc_start: 0.8929 (t0) cc_final: 0.8724 (t0) REVERT: D 132 ASP cc_start: 0.8893 (t0) cc_final: 0.8640 (t0) REVERT: D 157 ASP cc_start: 0.8784 (m-30) cc_final: 0.8566 (m-30) REVERT: D 186 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8341 (tm-30) REVERT: D 251 TYR cc_start: 0.8676 (m-80) cc_final: 0.8355 (m-80) outliers start: 12 outliers final: 4 residues processed: 206 average time/residue: 0.0918 time to fit residues: 25.7182 Evaluate side-chains 175 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 171 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain D residue 23 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 GLN D 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.062682 restraints weight = 23358.480| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 4.27 r_work: 0.2764 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 9048 Z= 0.294 Angle : 0.746 13.874 12212 Z= 0.360 Chirality : 0.044 0.203 1408 Planarity : 0.004 0.030 1544 Dihedral : 12.702 149.642 1300 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.40 % Allowed : 21.17 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.23 (0.26), residues: 1108 helix: 1.30 (0.21), residues: 596 sheet: -0.10 (0.38), residues: 188 loop : 0.76 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 129 TYR 0.025 0.002 TYR C 106 PHE 0.026 0.002 PHE H 80 TRP 0.008 0.002 TRP A 174 HIS 0.004 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00666 ( 9048) covalent geometry : angle 0.74572 (12212) hydrogen bonds : bond 0.05191 ( 460) hydrogen bonds : angle 4.29712 ( 1212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.231 Fit side-chains REVERT: C 68 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8532 (tm-30) REVERT: C 110 MET cc_start: 0.8923 (mtt) cc_final: 0.8669 (mtt) REVERT: C 115 ASP cc_start: 0.9049 (t0) cc_final: 0.8757 (t0) REVERT: C 121 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8157 (mmm) REVERT: C 132 ASP cc_start: 0.9436 (m-30) cc_final: 0.8790 (t0) REVERT: C 239 MET cc_start: 0.8682 (mmm) cc_final: 0.7895 (tpp) REVERT: A 68 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8504 (tm-30) REVERT: A 104 MET cc_start: 0.9577 (tpt) cc_final: 0.9363 (mmm) REVERT: A 110 MET cc_start: 0.8963 (mtt) cc_final: 0.8740 (mtt) REVERT: A 115 ASP cc_start: 0.9076 (t0) cc_final: 0.8779 (t0) REVERT: A 121 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8178 (mmm) REVERT: A 239 MET cc_start: 0.8611 (mmm) cc_final: 0.7861 (tpp) REVERT: A 287 TRP cc_start: 0.8094 (m-10) cc_final: 0.7759 (m-10) REVERT: B 115 ASP cc_start: 0.9061 (t0) cc_final: 0.8776 (t0) REVERT: B 121 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8081 (mmm) REVERT: B 239 MET cc_start: 0.8747 (mmm) cc_final: 0.7977 (tpp) REVERT: B 248 ASN cc_start: 0.9354 (t0) cc_final: 0.9145 (t0) REVERT: B 287 TRP cc_start: 0.8093 (m-10) cc_final: 0.7747 (m-10) REVERT: D 68 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8560 (tm-30) REVERT: D 115 ASP cc_start: 0.9079 (t0) cc_final: 0.8797 (t0) REVERT: D 121 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8117 (mmm) REVERT: D 239 MET cc_start: 0.8685 (mmm) cc_final: 0.7915 (tpp) REVERT: D 287 TRP cc_start: 0.8060 (m-10) cc_final: 0.7754 (m-10) REVERT: H 72 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.7334 (t80) outliers start: 32 outliers final: 15 residues processed: 187 average time/residue: 0.0885 time to fit residues: 22.1999 Evaluate side-chains 183 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 104 optimal weight: 0.0170 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.086808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.065564 restraints weight = 23112.021| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.18 r_work: 0.2828 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9048 Z= 0.143 Angle : 0.645 14.750 12212 Z= 0.304 Chirality : 0.041 0.146 1408 Planarity : 0.003 0.029 1544 Dihedral : 11.946 134.253 1300 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 3.30 % Allowed : 21.60 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.52 (0.26), residues: 1108 helix: 1.50 (0.21), residues: 596 sheet: -0.05 (0.39), residues: 188 loop : 1.03 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 134 TYR 0.027 0.002 TYR D 106 PHE 0.030 0.002 PHE F 80 TRP 0.015 0.001 TRP C 287 HIS 0.003 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9048) covalent geometry : angle 0.64521 (12212) hydrogen bonds : bond 0.04103 ( 460) hydrogen bonds : angle 3.73690 ( 1212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.229 Fit side-chains REVERT: C 68 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8538 (tm-30) REVERT: C 83 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9210 (mp) REVERT: C 115 ASP cc_start: 0.9015 (t0) cc_final: 0.8709 (t0) REVERT: C 121 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8160 (mmm) REVERT: C 219 LYS cc_start: 0.8723 (mttt) cc_final: 0.8510 (mtmt) REVERT: C 239 MET cc_start: 0.8707 (mmm) cc_final: 0.8275 (tpp) REVERT: A 68 GLN cc_start: 0.9015 (tm-30) cc_final: 0.8542 (tm-30) REVERT: A 85 LYS cc_start: 0.9388 (ptmm) cc_final: 0.9165 (ptpp) REVERT: A 115 ASP cc_start: 0.9016 (t0) cc_final: 0.8706 (t0) REVERT: A 121 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8154 (mmm) REVERT: A 239 MET cc_start: 0.8647 (mmm) cc_final: 0.8258 (tpp) REVERT: B 83 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9098 (mp) REVERT: B 110 MET cc_start: 0.8696 (mtm) cc_final: 0.8425 (mtm) REVERT: B 115 ASP cc_start: 0.9007 (t0) cc_final: 0.8710 (t0) REVERT: B 121 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8027 (mmm) REVERT: B 239 MET cc_start: 0.8741 (mmm) cc_final: 0.7986 (tpp) REVERT: B 248 ASN cc_start: 0.9304 (t0) cc_final: 0.9083 (t0) REVERT: B 287 TRP cc_start: 0.8058 (m-10) cc_final: 0.7579 (m-10) REVERT: D 68 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8569 (tm-30) REVERT: D 83 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9108 (mp) REVERT: D 115 ASP cc_start: 0.9014 (t0) cc_final: 0.8720 (t0) REVERT: D 121 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8147 (mmm) REVERT: D 239 MET cc_start: 0.8716 (mmm) cc_final: 0.7960 (tpp) REVERT: D 287 TRP cc_start: 0.8009 (m-10) cc_final: 0.7546 (m-10) outliers start: 31 outliers final: 11 residues processed: 199 average time/residue: 0.0806 time to fit residues: 21.9527 Evaluate side-chains 183 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 285 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 48 optimal weight: 0.0980 chunk 38 optimal weight: 3.9990 chunk 110 optimal weight: 0.3980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN D 248 ASN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.087144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.065959 restraints weight = 22833.504| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 4.17 r_work: 0.2838 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9048 Z= 0.132 Angle : 0.624 8.647 12212 Z= 0.295 Chirality : 0.040 0.133 1408 Planarity : 0.003 0.026 1544 Dihedral : 11.347 133.858 1300 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.19 % Allowed : 21.06 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.74 (0.26), residues: 1108 helix: 1.63 (0.21), residues: 596 sheet: 0.06 (0.39), residues: 188 loop : 1.22 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 6 TYR 0.020 0.002 TYR A 106 PHE 0.022 0.002 PHE E 80 TRP 0.019 0.002 TRP A 287 HIS 0.002 0.000 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9048) covalent geometry : angle 0.62439 (12212) hydrogen bonds : bond 0.03771 ( 460) hydrogen bonds : angle 3.59839 ( 1212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.301 Fit side-chains REVERT: C 68 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8532 (tm-30) REVERT: C 83 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9202 (mp) REVERT: C 115 ASP cc_start: 0.8997 (t0) cc_final: 0.8709 (t0) REVERT: C 121 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8157 (mmm) REVERT: C 239 MET cc_start: 0.8682 (mmm) cc_final: 0.8206 (tpp) REVERT: A 85 LYS cc_start: 0.9389 (ptmm) cc_final: 0.9137 (ptpp) REVERT: A 115 ASP cc_start: 0.8995 (t0) cc_final: 0.8701 (t0) REVERT: A 121 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.8268 (mmm) REVERT: A 239 MET cc_start: 0.8638 (mmm) cc_final: 0.8203 (tpp) REVERT: B 68 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8863 (tm-30) REVERT: B 115 ASP cc_start: 0.8990 (t0) cc_final: 0.8726 (t0) REVERT: B 121 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.8167 (mmm) REVERT: B 219 LYS cc_start: 0.8578 (mttt) cc_final: 0.8354 (mtmt) REVERT: B 239 MET cc_start: 0.8694 (mmm) cc_final: 0.8286 (tpp) REVERT: B 287 TRP cc_start: 0.8186 (m-10) cc_final: 0.7678 (m-10) REVERT: D 68 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8571 (tm-30) REVERT: D 83 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9063 (mp) REVERT: D 115 ASP cc_start: 0.8930 (t0) cc_final: 0.8686 (t0) REVERT: D 121 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8116 (mmm) REVERT: D 219 LYS cc_start: 0.8693 (mttt) cc_final: 0.8394 (mtmt) REVERT: D 239 MET cc_start: 0.8702 (mmm) cc_final: 0.8266 (tpp) REVERT: D 287 TRP cc_start: 0.8144 (m-10) cc_final: 0.7658 (m-10) outliers start: 30 outliers final: 14 residues processed: 191 average time/residue: 0.0875 time to fit residues: 22.7890 Evaluate side-chains 180 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 285 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN B 248 ASN D 223 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.084180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.063163 restraints weight = 23415.105| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 4.07 r_work: 0.2786 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9048 Z= 0.278 Angle : 0.721 9.857 12212 Z= 0.342 Chirality : 0.042 0.168 1408 Planarity : 0.003 0.028 1544 Dihedral : 11.401 131.825 1300 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.51 % Allowed : 22.55 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.42 (0.26), residues: 1108 helix: 1.48 (0.21), residues: 620 sheet: 0.06 (0.40), residues: 168 loop : 0.63 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 6 TYR 0.021 0.002 TYR A 106 PHE 0.025 0.002 PHE G 80 TRP 0.050 0.003 TRP C 287 HIS 0.002 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00632 ( 9048) covalent geometry : angle 0.72080 (12212) hydrogen bonds : bond 0.04600 ( 460) hydrogen bonds : angle 4.01133 ( 1212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: C 115 ASP cc_start: 0.9070 (t0) cc_final: 0.8756 (t0) REVERT: C 121 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8339 (mmm) REVERT: C 239 MET cc_start: 0.8828 (mmm) cc_final: 0.8330 (tpp) REVERT: A 104 MET cc_start: 0.9575 (tpt) cc_final: 0.9355 (mmm) REVERT: A 115 ASP cc_start: 0.9066 (t0) cc_final: 0.8759 (t0) REVERT: A 121 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.8249 (mmm) REVERT: A 219 LYS cc_start: 0.8593 (mttt) cc_final: 0.8384 (mtmt) REVERT: A 239 MET cc_start: 0.8790 (mmm) cc_final: 0.8296 (tpp) REVERT: B 115 ASP cc_start: 0.9028 (t0) cc_final: 0.8715 (t0) REVERT: B 121 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8159 (mmm) REVERT: B 239 MET cc_start: 0.8819 (mmm) cc_final: 0.8395 (tpp) REVERT: D 83 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9156 (mp) REVERT: D 115 ASP cc_start: 0.8993 (t0) cc_final: 0.8725 (t0) REVERT: D 121 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8157 (mmm) REVERT: D 239 MET cc_start: 0.8802 (mmm) cc_final: 0.8366 (tpp) outliers start: 33 outliers final: 20 residues processed: 176 average time/residue: 0.0914 time to fit residues: 21.9849 Evaluate side-chains 188 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain H residue 83 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.086634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.065156 restraints weight = 23428.735| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 4.31 r_work: 0.2810 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9048 Z= 0.142 Angle : 0.650 7.149 12212 Z= 0.308 Chirality : 0.040 0.141 1408 Planarity : 0.003 0.027 1544 Dihedral : 11.081 129.664 1300 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.77 % Allowed : 24.36 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.59 (0.26), residues: 1108 helix: 1.56 (0.22), residues: 620 sheet: 0.21 (0.41), residues: 168 loop : 0.76 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 6 TYR 0.015 0.002 TYR E 72 PHE 0.027 0.002 PHE G 80 TRP 0.044 0.004 TRP C 287 HIS 0.001 0.000 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9048) covalent geometry : angle 0.65025 (12212) hydrogen bonds : bond 0.03853 ( 460) hydrogen bonds : angle 3.61081 ( 1212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: C 115 ASP cc_start: 0.9006 (t0) cc_final: 0.8734 (t0) REVERT: C 121 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.8302 (mmm) REVERT: C 219 LYS cc_start: 0.8624 (mttt) cc_final: 0.8169 (mtmt) REVERT: C 239 MET cc_start: 0.8791 (mmm) cc_final: 0.8440 (tpp) REVERT: C 251 TYR cc_start: 0.8730 (m-80) cc_final: 0.8300 (m-80) REVERT: A 110 MET cc_start: 0.8732 (mtm) cc_final: 0.8488 (mtm) REVERT: A 115 ASP cc_start: 0.8989 (t0) cc_final: 0.8709 (t0) REVERT: A 121 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.8325 (mmm) REVERT: A 219 LYS cc_start: 0.8592 (mttt) cc_final: 0.8321 (mtmt) REVERT: A 239 MET cc_start: 0.8777 (mmm) cc_final: 0.8453 (tpp) REVERT: B 115 ASP cc_start: 0.8950 (t0) cc_final: 0.8676 (t0) REVERT: B 121 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.8218 (mmm) REVERT: B 239 MET cc_start: 0.8800 (mmm) cc_final: 0.8362 (tpp) REVERT: B 251 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.8628 (m-80) REVERT: D 83 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9069 (mp) REVERT: D 115 ASP cc_start: 0.8927 (t0) cc_final: 0.8659 (t0) REVERT: D 121 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.8222 (mmm) REVERT: D 239 MET cc_start: 0.8740 (mmm) cc_final: 0.8253 (tpp) REVERT: D 251 TYR cc_start: 0.8763 (m-80) cc_final: 0.8430 (m-80) outliers start: 26 outliers final: 11 residues processed: 188 average time/residue: 0.0900 time to fit residues: 23.0200 Evaluate side-chains 190 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 285 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.087633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.066127 restraints weight = 23201.025| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 4.29 r_work: 0.2832 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9048 Z= 0.129 Angle : 0.658 8.034 12212 Z= 0.312 Chirality : 0.040 0.135 1408 Planarity : 0.003 0.027 1544 Dihedral : 10.681 127.865 1300 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.34 % Allowed : 25.00 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.64 (0.26), residues: 1108 helix: 1.55 (0.21), residues: 620 sheet: 0.31 (0.42), residues: 168 loop : 0.85 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 8 TYR 0.017 0.002 TYR C 106 PHE 0.030 0.002 PHE E 80 TRP 0.055 0.005 TRP A 287 HIS 0.002 0.000 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9048) covalent geometry : angle 0.65838 (12212) hydrogen bonds : bond 0.03726 ( 460) hydrogen bonds : angle 3.51935 ( 1212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: C 115 ASP cc_start: 0.8979 (t0) cc_final: 0.8708 (t0) REVERT: C 121 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.8326 (mmm) REVERT: C 219 LYS cc_start: 0.8635 (mttt) cc_final: 0.8202 (mtmt) REVERT: C 239 MET cc_start: 0.8870 (mmm) cc_final: 0.8485 (tpp) REVERT: C 251 TYR cc_start: 0.8782 (m-80) cc_final: 0.8378 (m-80) REVERT: A 110 MET cc_start: 0.8744 (mtm) cc_final: 0.8499 (mtm) REVERT: A 115 ASP cc_start: 0.8948 (t0) cc_final: 0.8656 (t0) REVERT: A 121 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.8347 (mmm) REVERT: A 219 LYS cc_start: 0.8574 (mttt) cc_final: 0.8330 (mtmt) REVERT: A 239 MET cc_start: 0.8852 (mmm) cc_final: 0.8490 (tpp) REVERT: B 54 GLU cc_start: 0.8585 (mp0) cc_final: 0.7842 (pm20) REVERT: B 115 ASP cc_start: 0.8956 (t0) cc_final: 0.8700 (t0) REVERT: B 121 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8237 (mmm) REVERT: B 239 MET cc_start: 0.8752 (mmm) cc_final: 0.8266 (tpp) REVERT: B 251 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.8603 (m-80) REVERT: D 115 ASP cc_start: 0.8919 (t0) cc_final: 0.8654 (t0) REVERT: D 121 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.8282 (mmm) REVERT: D 239 MET cc_start: 0.8761 (mmm) cc_final: 0.8249 (tpp) REVERT: D 251 TYR cc_start: 0.8766 (m-80) cc_final: 0.8435 (m-80) outliers start: 22 outliers final: 10 residues processed: 180 average time/residue: 0.0896 time to fit residues: 22.1533 Evaluate side-chains 182 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 147 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 3.9990 chunk 99 optimal weight: 0.0670 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.086518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.065641 restraints weight = 23065.680| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 4.12 r_work: 0.2826 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9048 Z= 0.162 Angle : 0.703 13.889 12212 Z= 0.334 Chirality : 0.041 0.180 1408 Planarity : 0.003 0.028 1544 Dihedral : 10.478 126.858 1300 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.02 % Allowed : 25.43 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.73 (0.26), residues: 1108 helix: 1.61 (0.22), residues: 620 sheet: 0.36 (0.41), residues: 168 loop : 0.92 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 6 TYR 0.018 0.002 TYR G 72 PHE 0.027 0.002 PHE G 80 TRP 0.050 0.005 TRP B 287 HIS 0.002 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9048) covalent geometry : angle 0.70296 (12212) hydrogen bonds : bond 0.03892 ( 460) hydrogen bonds : angle 3.58029 ( 1212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.274 Fit side-chains REVERT: C 115 ASP cc_start: 0.8997 (t0) cc_final: 0.8690 (t0) REVERT: C 121 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.8323 (mmm) REVERT: C 186 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8574 (tm-30) REVERT: C 219 LYS cc_start: 0.8666 (mttt) cc_final: 0.8464 (mtmt) REVERT: C 239 MET cc_start: 0.8869 (mmm) cc_final: 0.8382 (tpp) REVERT: A 87 GLN cc_start: 0.8890 (pm20) cc_final: 0.8665 (pm20) REVERT: A 115 ASP cc_start: 0.8940 (t0) cc_final: 0.8655 (t0) REVERT: A 121 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8302 (mmm) REVERT: A 219 LYS cc_start: 0.8584 (mttt) cc_final: 0.8348 (mtmt) REVERT: A 239 MET cc_start: 0.8844 (mmm) cc_final: 0.8384 (tpp) REVERT: B 115 ASP cc_start: 0.8958 (t0) cc_final: 0.8698 (t0) REVERT: B 121 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.8287 (mmm) REVERT: B 239 MET cc_start: 0.8857 (mmm) cc_final: 0.8327 (tpp) REVERT: B 251 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.8619 (m-80) REVERT: D 115 ASP cc_start: 0.8940 (t0) cc_final: 0.8673 (t0) REVERT: D 121 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.8278 (mmm) REVERT: D 239 MET cc_start: 0.8768 (mmm) cc_final: 0.8348 (tpp) outliers start: 19 outliers final: 11 residues processed: 180 average time/residue: 0.0889 time to fit residues: 21.7811 Evaluate side-chains 184 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 223 GLN Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 121 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 0.3980 chunk 50 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.087106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.067135 restraints weight = 22767.809| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 4.00 r_work: 0.2846 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9048 Z= 0.190 Angle : 0.730 10.618 12212 Z= 0.352 Chirality : 0.041 0.227 1408 Planarity : 0.003 0.027 1544 Dihedral : 10.416 125.941 1300 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.02 % Allowed : 25.11 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.70 (0.26), residues: 1108 helix: 1.59 (0.22), residues: 620 sheet: 0.31 (0.41), residues: 168 loop : 0.91 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 8 TYR 0.022 0.002 TYR A 106 PHE 0.028 0.002 PHE G 80 TRP 0.064 0.006 TRP D 287 HIS 0.005 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 9048) covalent geometry : angle 0.72993 (12212) hydrogen bonds : bond 0.04135 ( 460) hydrogen bonds : angle 3.69188 ( 1212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.218 Fit side-chains REVERT: C 115 ASP cc_start: 0.9052 (t0) cc_final: 0.8724 (t0) REVERT: C 121 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.8275 (mmm) REVERT: C 239 MET cc_start: 0.8931 (mmm) cc_final: 0.8255 (ttm) REVERT: A 87 GLN cc_start: 0.8925 (pm20) cc_final: 0.8717 (pm20) REVERT: A 115 ASP cc_start: 0.8996 (t0) cc_final: 0.8686 (t0) REVERT: A 120 GLN cc_start: 0.9401 (tt0) cc_final: 0.9187 (tt0) REVERT: A 121 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.8305 (mmm) REVERT: A 219 LYS cc_start: 0.8546 (mttt) cc_final: 0.8303 (mtmt) REVERT: A 239 MET cc_start: 0.8864 (mmm) cc_final: 0.8222 (ttm) REVERT: B 38 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9007 (mp) REVERT: B 115 ASP cc_start: 0.8993 (t0) cc_final: 0.8726 (t0) REVERT: B 121 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.8252 (mmm) REVERT: B 131 LYS cc_start: 0.9353 (pttm) cc_final: 0.9142 (mmmt) REVERT: B 219 LYS cc_start: 0.8586 (mttt) cc_final: 0.8124 (ttpt) REVERT: B 239 MET cc_start: 0.8916 (mmm) cc_final: 0.8452 (tpp) REVERT: D 115 ASP cc_start: 0.8996 (t0) cc_final: 0.8717 (t0) REVERT: D 121 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.8183 (mmm) REVERT: D 131 LYS cc_start: 0.9360 (pttm) cc_final: 0.9152 (mmmt) REVERT: D 239 MET cc_start: 0.8870 (mmm) cc_final: 0.8459 (tpp) REVERT: D 251 TYR cc_start: 0.8633 (m-80) cc_final: 0.8313 (m-80) outliers start: 19 outliers final: 11 residues processed: 180 average time/residue: 0.0786 time to fit residues: 19.1849 Evaluate side-chains 184 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 121 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.086304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.066626 restraints weight = 22793.302| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 4.03 r_work: 0.2864 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9048 Z= 0.146 Angle : 0.701 11.548 12212 Z= 0.334 Chirality : 0.041 0.269 1408 Planarity : 0.003 0.027 1544 Dihedral : 10.165 124.368 1300 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.70 % Allowed : 25.74 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.76 (0.26), residues: 1108 helix: 1.61 (0.22), residues: 620 sheet: 0.33 (0.41), residues: 168 loop : 1.01 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 6 TYR 0.018 0.002 TYR C 106 PHE 0.027 0.002 PHE G 80 TRP 0.054 0.006 TRP D 287 HIS 0.006 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9048) covalent geometry : angle 0.70085 (12212) hydrogen bonds : bond 0.03849 ( 460) hydrogen bonds : angle 3.53251 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1709.82 seconds wall clock time: 30 minutes 5.96 seconds (1805.96 seconds total)