Starting phenix.real_space_refine on Fri Jul 3 12:06:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9egt_47997/07_2026/9egt_47997.cif Found real_map, /net/cci-nas-00/data/ceres_data/9egt_47997/07_2026/9egt_47997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9egt_47997/07_2026/9egt_47997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9egt_47997/07_2026/9egt_47997.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9egt_47997/07_2026/9egt_47997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9egt_47997/07_2026/9egt_47997.map" } resolution = 2.57 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= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 70 5.16 5 C 9205 2.51 5 N 2250 2.21 5 O 2639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14169 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2779 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 322} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.74, per 1000 atoms: 0.19 Number of scatterers: 14169 At special positions: 0 Unit cell: (90.625, 89.9, 109.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 70 16.00 O 2639 8.00 N 2250 7.00 C 9205 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: 1.10 Conformation dependent library (CDL) restraints added in 556.4 milliseconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 0 sheets defined 77.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.646A pdb=" N ALA A 10 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.571A pdb=" N LEU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 52 removed outlier: 3.569A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 Processing helix chain 'A' and resid 73 through 76 Processing helix chain 'A' and resid 77 through 99 Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.603A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.611A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 3.547A pdb=" N LEU A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.563A pdb=" N THR A 237 " --> pdb=" O PRO A 233 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 295 Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'B' and resid 6 through 10 removed outlier: 3.647A pdb=" N ALA B 10 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 removed outlier: 3.571A pdb=" N LEU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 52 removed outlier: 3.569A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 72 Processing helix chain 'B' and resid 73 through 76 Processing helix chain 'B' and resid 77 through 99 Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.604A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.610A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.547A pdb=" N LEU B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.562A pdb=" N THR B 237 " --> pdb=" O PRO B 233 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 295 Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.646A pdb=" N ALA C 10 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.571A pdb=" N LEU C 22 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS C 23 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 52 removed outlier: 3.569A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 72 Processing helix chain 'C' and resid 73 through 76 Processing helix chain 'C' and resid 77 through 99 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.604A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.611A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 removed outlier: 3.547A pdb=" N LEU C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.562A pdb=" N THR C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 295 Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'D' and resid 6 through 10 removed outlier: 3.647A pdb=" N ALA D 10 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 removed outlier: 3.571A pdb=" N LEU D 22 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS D 23 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 52 removed outlier: 3.569A pdb=" N LEU D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 72 Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 77 through 99 Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.603A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.612A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 removed outlier: 3.547A pdb=" N LEU D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.562A pdb=" N THR D 237 " --> pdb=" O PRO D 233 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 295 Processing helix chain 'D' and resid 306 through 324 Processing helix chain 'E' and resid 6 through 10 removed outlier: 3.647A pdb=" N ALA E 10 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 removed outlier: 3.570A pdb=" N LEU E 22 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 52 removed outlier: 3.570A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 72 Processing helix chain 'E' and resid 73 through 76 Processing helix chain 'E' and resid 77 through 99 Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.603A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.610A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.548A pdb=" N LEU E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.563A pdb=" N THR E 237 " --> pdb=" O PRO E 233 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 295 Processing helix chain 'E' and resid 306 through 324 935 hydrogen bonds defined for protein. 2730 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4250 1.34 - 1.46: 3099 1.46 - 1.57: 6856 1.57 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 14320 Sorted by residual: bond pdb=" C ARG D 130 " pdb=" O ARG D 130 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.29e-02 6.01e+03 6.37e-01 bond pdb=" CA ILE A 230 " pdb=" CB ILE A 230 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.36e-02 5.41e+03 6.20e-01 bond pdb=" C ARG E 130 " pdb=" O ARG E 130 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.29e-02 6.01e+03 6.13e-01 bond pdb=" CA ILE B 230 " pdb=" CB ILE B 230 " ideal model delta sigma weight residual 1.540 1.530 0.010 1.36e-02 5.41e+03 5.90e-01 bond pdb=" CA ILE E 230 " pdb=" CB ILE E 230 " ideal model delta sigma weight residual 1.540 1.530 0.010 1.36e-02 5.41e+03 5.47e-01 ... (remaining 14315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 18880 1.11 - 2.23: 502 2.23 - 3.34: 133 3.34 - 4.45: 25 4.45 - 5.56: 10 Bond angle restraints: 19550 Sorted by residual: angle pdb=" C PHE D 247 " pdb=" N PHE D 248 " pdb=" CA PHE D 248 " ideal model delta sigma weight residual 121.66 117.84 3.82 1.76e+00 3.23e-01 4.70e+00 angle pdb=" C PHE C 247 " pdb=" N PHE C 248 " pdb=" CA PHE C 248 " ideal model delta sigma weight residual 121.66 117.87 3.79 1.76e+00 3.23e-01 4.63e+00 angle pdb=" C PHE E 247 " pdb=" N PHE E 248 " pdb=" CA PHE E 248 " ideal model delta sigma weight residual 121.66 117.88 3.78 1.76e+00 3.23e-01 4.60e+00 angle pdb=" C PHE A 247 " pdb=" N PHE A 248 " pdb=" CA PHE A 248 " ideal model delta sigma weight residual 121.66 117.89 3.77 1.76e+00 3.23e-01 4.58e+00 angle pdb=" C PHE B 247 " pdb=" N PHE B 248 " pdb=" CA PHE B 248 " ideal model delta sigma weight residual 121.66 117.90 3.76 1.76e+00 3.23e-01 4.57e+00 ... (remaining 19545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 7534 15.93 - 31.85: 521 31.85 - 47.78: 155 47.78 - 63.70: 25 63.70 - 79.63: 15 Dihedral angle restraints: 8250 sinusoidal: 3250 harmonic: 5000 Sorted by residual: dihedral pdb=" CA ARG D 313 " pdb=" CB ARG D 313 " pdb=" CG ARG D 313 " pdb=" CD ARG D 313 " ideal model delta sinusoidal sigma weight residual -60.00 -117.03 57.03 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA ARG E 313 " pdb=" CB ARG E 313 " pdb=" CG ARG E 313 " pdb=" CD ARG E 313 " ideal model delta sinusoidal sigma weight residual -60.00 -117.02 57.02 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA ARG B 313 " pdb=" CB ARG B 313 " pdb=" CG ARG B 313 " pdb=" CD ARG B 313 " ideal model delta sinusoidal sigma weight residual -60.00 -117.02 57.02 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 8247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1451 0.032 - 0.063: 552 0.063 - 0.095: 113 0.095 - 0.127: 40 0.127 - 0.159: 14 Chirality restraints: 2170 Sorted by residual: chirality pdb=" CA ILE C 232 " pdb=" N ILE C 232 " pdb=" C ILE C 232 " pdb=" CB ILE C 232 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA PHE E 248 " pdb=" N PHE E 248 " pdb=" C PHE E 248 " pdb=" CB PHE E 248 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA ILE D 232 " pdb=" N ILE D 232 " pdb=" C ILE D 232 " pdb=" CB ILE D 232 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 2167 not shown) Planarity restraints: 2420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 248 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C PHE C 248 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE C 248 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU C 249 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 248 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C PHE D 248 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE D 248 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU D 249 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 248 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C PHE B 248 " -0.025 2.00e-02 2.50e+03 pdb=" O PHE B 248 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU B 249 " 0.009 2.00e-02 2.50e+03 ... (remaining 2417 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2446 2.76 - 3.30: 14068 3.30 - 3.83: 26781 3.83 - 4.37: 32815 4.37 - 4.90: 53574 Nonbonded interactions: 129684 Sorted by model distance: nonbonded pdb="CA CA A 500 " pdb=" O HOH A 604 " model vdw 2.231 3.250 nonbonded pdb="CA CA E 500 " pdb=" O HOH E 605 " model vdw 2.240 3.250 nonbonded pdb="CA CA B 500 " pdb=" O HOH B 604 " model vdw 2.246 3.250 nonbonded pdb="CA CA C 500 " pdb=" O HOH C 603 " model vdw 2.254 3.250 nonbonded pdb="CA CA D 500 " pdb=" O HOH D 606 " model vdw 2.256 3.250 ... (remaining 129679 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 11.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.130 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 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 : 0.002 0.021 14320 Z= 0.118 Angle : 0.479 5.564 19550 Z= 0.258 Chirality : 0.037 0.159 2170 Planarity : 0.004 0.030 2420 Dihedral : 12.753 79.630 5030 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.67 % Allowed : 5.03 % Favored : 94.30 % 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 are not related in a simple way. whole: 0.41 (0.20), residues: 1680 helix: 0.73 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -0.60 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 150 TYR 0.016 0.001 TYR E 97 PHE 0.020 0.001 PHE D 248 TRP 0.012 0.001 TRP A 94 HIS 0.003 0.001 HIS E 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.12 (14320) covalent geometry : angle 0.47897 / 0.26 (19550) hydrogen bonds : bond 0.13348 / 8.75 ( 935) hydrogen bonds : angle 5.75750 / 4.24 ( 2730) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 241 time to evaluate : 0.453 Fit side-chains REVERT: B 70 ASP cc_start: 0.8010 (t0) cc_final: 0.7494 (t0) REVERT: B 332 MET cc_start: 0.8688 (ttp) cc_final: 0.8344 (ttp) REVERT: C 60 LEU cc_start: 0.7771 (tp) cc_final: 0.7402 (tm) REVERT: D 60 LEU cc_start: 0.7761 (tp) cc_final: 0.7465 (tm) REVERT: D 115 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7809 (mm-30) REVERT: D 300 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8388 (mt-10) outliers start: 10 outliers final: 0 residues processed: 251 average time/residue: 0.6277 time to fit residues: 172.4499 Evaluate side-chains 214 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.2980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 GLN A 212 ASN B 133 ASN B 212 ASN C 212 ASN D 159 GLN D 212 ASN E 159 GLN E 212 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.131692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109706 restraints weight = 14192.205| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.11 r_work: 0.3254 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14320 Z= 0.201 Angle : 0.564 6.689 19550 Z= 0.303 Chirality : 0.041 0.159 2170 Planarity : 0.005 0.034 2420 Dihedral : 4.300 17.202 1865 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.41 % Allowed : 8.72 % Favored : 89.87 % 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 are not related in a simple way. whole: 1.25 (0.20), residues: 1680 helix: 1.45 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.44 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 313 TYR 0.024 0.002 TYR D 97 PHE 0.027 0.002 PHE E 248 TRP 0.015 0.002 TRP A 94 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (14320) covalent geometry : angle 0.56378 / 0.30 (19550) hydrogen bonds : bond 0.06596 / 4.31 ( 935) hydrogen bonds : angle 4.63035 / 3.39 ( 2730) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.551 Fit side-chains REVERT: B 57 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7365 (pt0) outliers start: 21 outliers final: 6 residues processed: 217 average time/residue: 0.5939 time to fit residues: 141.4180 Evaluate side-chains 199 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 192 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain E residue 57 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 33 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 GLN A 296 ASN B 296 ASN D 159 GLN E 159 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113543 restraints weight = 14528.333| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.10 r_work: 0.3273 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14320 Z= 0.163 Angle : 0.516 6.298 19550 Z= 0.278 Chirality : 0.039 0.158 2170 Planarity : 0.004 0.028 2420 Dihedral : 4.195 16.037 1865 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.28 % Allowed : 10.20 % Favored : 87.52 % 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 are not related in a simple way. whole: 1.43 (0.20), residues: 1680 helix: 1.63 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.50 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 126 TYR 0.026 0.002 TYR C 33 PHE 0.026 0.002 PHE A 248 TRP 0.014 0.002 TRP E 94 HIS 0.003 0.001 HIS E 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (14320) covalent geometry : angle 0.51577 / 0.28 (19550) hydrogen bonds : bond 0.05936 / 3.89 ( 935) hydrogen bonds : angle 4.43478 / 3.24 ( 2730) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.523 Fit side-chains REVERT: C 55 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7740 (m) REVERT: D 57 GLU cc_start: 0.7355 (pt0) cc_final: 0.7112 (pp20) REVERT: E 57 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7219 (pt0) REVERT: E 203 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8450 (t70) outliers start: 34 outliers final: 9 residues processed: 223 average time/residue: 0.4984 time to fit residues: 122.4661 Evaluate side-chains 202 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 203 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 74 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 GLN D 159 GLN E 159 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110268 restraints weight = 14326.815| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.12 r_work: 0.3257 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14320 Z= 0.173 Angle : 0.532 6.513 19550 Z= 0.285 Chirality : 0.039 0.160 2170 Planarity : 0.004 0.029 2420 Dihedral : 4.225 16.434 1865 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.68 % Allowed : 11.41 % Favored : 86.91 % 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 are not related in a simple way. whole: 1.49 (0.20), residues: 1680 helix: 1.68 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.49 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 313 TYR 0.028 0.002 TYR C 33 PHE 0.027 0.002 PHE A 248 TRP 0.015 0.002 TRP B 94 HIS 0.003 0.001 HIS E 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (14320) covalent geometry : angle 0.53197 / 0.29 (19550) hydrogen bonds : bond 0.06032 / 3.95 ( 935) hydrogen bonds : angle 4.40854 / 3.22 ( 2730) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.424 Fit side-chains REVERT: B 57 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7371 (pt0) REVERT: C 324 GLU cc_start: 0.8373 (mp0) cc_final: 0.8160 (mp0) REVERT: E 57 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7350 (pt0) REVERT: E 203 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8430 (t70) outliers start: 25 outliers final: 15 residues processed: 207 average time/residue: 0.5348 time to fit residues: 121.3661 Evaluate side-chains 201 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 203 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 44 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 GLN D 159 GLN E 159 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.132972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110977 restraints weight = 14593.786| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.10 r_work: 0.3228 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 14320 Z= 0.205 Angle : 0.563 6.829 19550 Z= 0.301 Chirality : 0.041 0.164 2170 Planarity : 0.005 0.029 2420 Dihedral : 4.344 16.776 1865 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.75 % Allowed : 11.01 % Favored : 86.24 % 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 are not related in a simple way. whole: 1.37 (0.20), residues: 1680 helix: 1.55 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -0.56 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 126 TYR 0.029 0.002 TYR C 33 PHE 0.028 0.002 PHE E 248 TRP 0.015 0.002 TRP B 94 HIS 0.004 0.001 HIS E 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (14320) covalent geometry : angle 0.56302 / 0.30 (19550) hydrogen bonds : bond 0.06347 / 4.15 ( 935) hydrogen bonds : angle 4.46701 / 3.27 ( 2730) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.347 Fit side-chains REVERT: A 300 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8397 (mt-10) REVERT: C 130 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8255 (ttp80) REVERT: E 203 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8438 (t70) outliers start: 41 outliers final: 19 residues processed: 218 average time/residue: 0.5400 time to fit residues: 128.7418 Evaluate side-chains 201 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 231 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 44 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 GLN D 159 GLN E 159 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.135020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113153 restraints weight = 14535.610| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.10 r_work: 0.3258 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14320 Z= 0.161 Angle : 0.520 6.351 19550 Z= 0.279 Chirality : 0.039 0.159 2170 Planarity : 0.004 0.029 2420 Dihedral : 4.203 16.319 1865 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.01 % Allowed : 12.89 % Favored : 85.10 % 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 are not related in a simple way. whole: 1.50 (0.20), residues: 1680 helix: 1.75 (0.15), residues: 1145 sheet: None (None), residues: 0 loop : -0.64 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.029 0.002 TYR C 33 PHE 0.026 0.002 PHE E 248 TRP 0.015 0.002 TRP B 94 HIS 0.003 0.001 HIS E 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (14320) covalent geometry : angle 0.52021 / 0.28 (19550) hydrogen bonds : bond 0.05871 / 3.85 ( 935) hydrogen bonds : angle 4.38354 / 3.20 ( 2730) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.355 Fit side-chains REVERT: B 203 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8490 (t70) REVERT: C 57 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7345 (pt0) REVERT: D 235 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8525 (m) REVERT: D 290 VAL cc_start: 0.8556 (t) cc_final: 0.8349 (m) REVERT: E 57 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7343 (pt0) REVERT: E 203 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8438 (t70) outliers start: 30 outliers final: 15 residues processed: 213 average time/residue: 0.5614 time to fit residues: 130.7163 Evaluate side-chains 202 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 287 TRP Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 231 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 73 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 158 optimal weight: 0.0270 chunk 64 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 GLN D 159 GLN E 159 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114467 restraints weight = 14514.666| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.10 r_work: 0.3275 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14320 Z= 0.145 Angle : 0.502 6.194 19550 Z= 0.270 Chirality : 0.038 0.158 2170 Planarity : 0.004 0.029 2420 Dihedral : 4.100 15.680 1865 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.01 % Allowed : 13.49 % Favored : 84.50 % 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 are not related in a simple way. whole: 1.62 (0.20), residues: 1680 helix: 1.82 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.55 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.030 0.002 TYR C 33 PHE 0.024 0.002 PHE D 84 TRP 0.014 0.002 TRP A 94 HIS 0.003 0.000 HIS E 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (14320) covalent geometry : angle 0.50160 / 0.27 (19550) hydrogen bonds : bond 0.05630 / 3.69 ( 935) hydrogen bonds : angle 4.33836 / 3.17 ( 2730) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.648 Fit side-chains REVERT: B 203 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8487 (t70) REVERT: B 290 VAL cc_start: 0.8625 (m) cc_final: 0.8423 (t) REVERT: C 57 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7314 (pt0) REVERT: E 203 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8421 (t70) REVERT: E 290 VAL cc_start: 0.8587 (t) cc_final: 0.8380 (m) outliers start: 30 outliers final: 14 residues processed: 215 average time/residue: 0.5131 time to fit residues: 121.3930 Evaluate side-chains 200 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 336 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN A 159 GLN C 58 GLN D 159 GLN E 159 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113118 restraints weight = 14427.915| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.09 r_work: 0.3263 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14320 Z= 0.169 Angle : 0.528 6.498 19550 Z= 0.282 Chirality : 0.039 0.161 2170 Planarity : 0.004 0.030 2420 Dihedral : 4.179 16.111 1865 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.68 % Allowed : 13.89 % Favored : 84.43 % 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 are not related in a simple way. whole: 1.56 (0.20), residues: 1680 helix: 1.80 (0.15), residues: 1145 sheet: None (None), residues: 0 loop : -0.62 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 105 TYR 0.031 0.002 TYR C 33 PHE 0.025 0.002 PHE E 248 TRP 0.014 0.002 TRP A 94 HIS 0.003 0.001 HIS E 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (14320) covalent geometry : angle 0.52788 / 0.28 (19550) hydrogen bonds : bond 0.05906 / 3.87 ( 935) hydrogen bonds : angle 4.38107 / 3.20 ( 2730) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.458 Fit side-chains REVERT: B 203 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8480 (t70) REVERT: C 130 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8307 (ttp80) REVERT: D 57 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7262 (pt0) REVERT: E 203 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8411 (t70) REVERT: E 290 VAL cc_start: 0.8662 (t) cc_final: 0.8458 (m) outliers start: 25 outliers final: 13 residues processed: 203 average time/residue: 0.6023 time to fit residues: 133.8148 Evaluate side-chains 198 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 336 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 GLN D 159 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113758 restraints weight = 14436.464| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.09 r_work: 0.3276 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14320 Z= 0.159 Angle : 0.521 6.225 19550 Z= 0.278 Chirality : 0.039 0.161 2170 Planarity : 0.004 0.030 2420 Dihedral : 4.147 15.779 1865 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.41 % Allowed : 14.30 % Favored : 84.30 % 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 are not related in a simple way. whole: 1.57 (0.20), residues: 1680 helix: 1.81 (0.15), residues: 1145 sheet: None (None), residues: 0 loop : -0.63 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 105 TYR 0.032 0.002 TYR C 33 PHE 0.024 0.002 PHE A 248 TRP 0.014 0.002 TRP E 94 HIS 0.003 0.001 HIS E 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (14320) covalent geometry : angle 0.52051 / 0.28 (19550) hydrogen bonds : bond 0.05787 / 3.79 ( 935) hydrogen bonds : angle 4.35915 / 3.19 ( 2730) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.684 Fit side-chains REVERT: B 203 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8494 (t70) REVERT: D 57 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7281 (pt0) REVERT: E 203 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8420 (t70) outliers start: 21 outliers final: 13 residues processed: 201 average time/residue: 0.6075 time to fit residues: 133.8256 Evaluate side-chains 197 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 336 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 75 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 GLN D 159 GLN E 159 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.132038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110038 restraints weight = 14514.933| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.09 r_work: 0.3213 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14320 Z= 0.239 Angle : 0.601 7.014 19550 Z= 0.319 Chirality : 0.043 0.169 2170 Planarity : 0.005 0.031 2420 Dihedral : 4.438 17.069 1865 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.41 % Allowed : 14.30 % Favored : 84.30 % 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 are not related in a simple way. whole: 1.33 (0.20), residues: 1680 helix: 1.60 (0.15), residues: 1145 sheet: None (None), residues: 0 loop : -0.64 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 313 TYR 0.034 0.002 TYR C 33 PHE 0.029 0.002 PHE E 248 TRP 0.013 0.002 TRP E 94 HIS 0.003 0.001 HIS E 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.24 (14320) covalent geometry : angle 0.60060 / 0.32 (19550) hydrogen bonds : bond 0.06617 / 4.32 ( 935) hydrogen bonds : angle 4.52595 / 3.31 ( 2730) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.584 Fit side-chains REVERT: B 290 VAL cc_start: 0.8724 (m) cc_final: 0.8502 (t) REVERT: C 290 VAL cc_start: 0.8753 (m) cc_final: 0.8551 (t) REVERT: C 300 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8375 (mt-10) REVERT: E 203 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8432 (t70) REVERT: E 300 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8411 (mt-10) outliers start: 21 outliers final: 10 residues processed: 193 average time/residue: 0.6383 time to fit residues: 134.8809 Evaluate side-chains 190 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 287 TRP Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 300 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 chunk 116 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 144 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 114 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 GLN D 159 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113722 restraints weight = 14410.529| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.09 r_work: 0.3275 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14320 Z= 0.153 Angle : 0.522 6.217 19550 Z= 0.279 Chirality : 0.039 0.159 2170 Planarity : 0.004 0.030 2420 Dihedral : 4.201 15.981 1865 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.01 % Allowed : 14.77 % Favored : 84.23 % 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 are not related in a simple way. whole: 1.45 (0.20), residues: 1680 helix: 1.72 (0.15), residues: 1145 sheet: None (None), residues: 0 loop : -0.68 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 105 TYR 0.031 0.002 TYR C 33 PHE 0.026 0.002 PHE E 248 TRP 0.014 0.002 TRP B 94 HIS 0.003 0.000 HIS E 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (14320) covalent geometry : angle 0.52190 / 0.28 (19550) hydrogen bonds : bond 0.05781 / 3.79 ( 935) hydrogen bonds : angle 4.38432 / 3.20 ( 2730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4371.63 seconds wall clock time: 75 minutes 35.04 seconds (4535.04 seconds total)