Starting phenix.real_space_refine on Thu Sep 18 04:35:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9egt_47997/09_2025/9egt_47997.cif Found real_map, /net/cci-nas-00/data/ceres_data/9egt_47997/09_2025/9egt_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9egt_47997/09_2025/9egt_47997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9egt_47997/09_2025/9egt_47997.map" model { file = "/net/cci-nas-00/data/ceres_data/9egt_47997/09_2025/9egt_47997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9egt_47997/09_2025/9egt_47997.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 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: 1.87, per 1000 atoms: 0.13 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: 1.05 Conformation dependent library (CDL) restraints added in 566.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.41 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: 2.26 Time building geometry restraints manager: 1.36 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 2.510 nonbonded pdb="CA CA E 500 " pdb=" O HOH E 605 " model vdw 2.240 2.510 nonbonded pdb="CA CA B 500 " pdb=" O HOH B 604 " model vdw 2.246 2.510 nonbonded pdb="CA CA C 500 " pdb=" O HOH C 603 " model vdw 2.254 2.510 nonbonded pdb="CA CA D 500 " pdb=" O HOH D 606 " model vdw 2.256 2.510 ... (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: 0.04 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: 12.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.390 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:5.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 aren 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 covalent geometry : bond 0.00225 (14320) covalent geometry : angle 0.47897 (19550) hydrogen bonds : bond 0.13348 ( 935) hydrogen bonds : angle 5.75750 ( 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 : 0.545 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: 0.6477 time to fit residues: 176.7558 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 : 0.563 ------------------------------------------------------------------------------- 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: 0.8980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.2980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3573 r_free = 0.3573 target = 0.133532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111492 restraints weight = 14338.218| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.09 r_work: 0.3237 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14320 Z= 0.202 Angle : 0.568 6.686 19550 Z= 0.306 Chirality : 0.041 0.160 2170 Planarity : 0.005 0.036 2420 Dihedral : 4.321 17.405 1865 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.48 % Allowed : 8.46 % Favored : 90.07 % 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: 1.32 (0.20), residues: 1680 helix: 1.50 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.43 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 313 TYR 0.026 0.002 TYR D 97 PHE 0.028 0.002 PHE E 248 TRP 0.016 0.002 TRP A 94 HIS 0.004 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00456 (14320) covalent geometry : angle 0.56847 (19550) hydrogen bonds : bond 0.06478 ( 935) hydrogen bonds : angle 4.57874 ( 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 227 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.574 Fit side-chains REVERT: D 268 GLU cc_start: 0.7906 (mp0) cc_final: 0.7692 (mp0) outliers start: 22 outliers final: 7 residues processed: 219 average time/residue: 0.6418 time to fit residues: 153.6651 Evaluate side-chains 200 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 193 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 16 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3549 r_free = 0.3549 target = 0.131766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109651 restraints weight = 14530.034| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.09 r_work: 0.3212 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14320 Z= 0.227 Angle : 0.586 7.063 19550 Z= 0.313 Chirality : 0.042 0.164 2170 Planarity : 0.005 0.036 2420 Dihedral : 4.458 17.138 1865 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.82 % Allowed : 9.60 % Favored : 87.58 % 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: 1.26 (0.20), residues: 1680 helix: 1.43 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.37 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 313 TYR 0.028 0.002 TYR C 97 PHE 0.030 0.002 PHE E 248 TRP 0.016 0.002 TRP B 94 HIS 0.004 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00525 (14320) covalent geometry : angle 0.58611 (19550) hydrogen bonds : bond 0.06671 ( 935) hydrogen bonds : angle 4.57670 ( 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 232 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 0.708 Fit side-chains REVERT: A 57 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7300 (pp20) REVERT: B 57 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7367 (pp20) REVERT: B 130 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8539 (ttp80) REVERT: D 57 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7124 (pp20) REVERT: E 203 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8465 (t70) outliers start: 42 outliers final: 13 residues processed: 223 average time/residue: 0.7002 time to fit residues: 170.4706 Evaluate side-chains 204 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU 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 57 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 130 ARG 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 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 336 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 129 ILE 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: 0.9980 chunk 108 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 99 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: 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 = 0.3568 r_free = 0.3568 target = 0.133189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111119 restraints weight = 14470.777| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.10 r_work: 0.3232 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14320 Z= 0.180 Angle : 0.548 6.718 19550 Z= 0.294 Chirality : 0.040 0.160 2170 Planarity : 0.005 0.029 2420 Dihedral : 4.340 16.604 1865 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.01 % Allowed : 11.21 % Favored : 86.78 % 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: 1.41 (0.20), residues: 1680 helix: 1.61 (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 B 313 TYR 0.026 0.002 TYR C 33 PHE 0.028 0.002 PHE E 248 TRP 0.016 0.002 TRP B 94 HIS 0.003 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00405 (14320) covalent geometry : angle 0.54763 (19550) hydrogen bonds : bond 0.06181 ( 935) hydrogen bonds : angle 4.45159 ( 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 219 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.622 Fit side-chains REVERT: A 300 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8433 (mt-10) REVERT: B 57 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7339 (pp20) REVERT: E 57 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7409 (pt0) REVERT: E 203 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8459 (t70) REVERT: E 300 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8437 (mt-10) outliers start: 30 outliers final: 11 residues processed: 211 average time/residue: 0.7579 time to fit residues: 173.3572 Evaluate side-chains 200 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 300 GLU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 129 ILE 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 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 300 GLU 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: 0.9990 chunk 160 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN D 159 GLN E 11 ASN E 159 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111397 restraints weight = 14540.781| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.10 r_work: 0.3236 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14320 Z= 0.176 Angle : 0.539 6.674 19550 Z= 0.289 Chirality : 0.039 0.161 2170 Planarity : 0.005 0.029 2420 Dihedral : 4.305 16.284 1865 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.28 % Allowed : 11.34 % Favored : 86.38 % 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: 1.50 (0.20), residues: 1680 helix: 1.69 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.50 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 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 covalent geometry : bond 0.00393 (14320) covalent geometry : angle 0.53914 (19550) hydrogen bonds : bond 0.06093 ( 935) hydrogen bonds : angle 4.41541 ( 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 223 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.581 Fit side-chains REVERT: A 57 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7311 (pp20) REVERT: B 57 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7342 (pp20) REVERT: C 130 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8268 (ttp80) REVERT: E 57 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7332 (pt0) REVERT: E 203 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8441 (t70) REVERT: E 300 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8437 (mt-10) outliers start: 34 outliers final: 12 residues processed: 216 average time/residue: 0.7265 time to fit residues: 170.5593 Evaluate side-chains 206 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU 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 57 GLU Chi-restraints excluded: chain B residue 129 ILE 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 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 300 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 44 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3580 r_free = 0.3580 target = 0.134040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112065 restraints weight = 14494.047| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.09 r_work: 0.3244 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14320 Z= 0.163 Angle : 0.525 6.447 19550 Z= 0.282 Chirality : 0.039 0.159 2170 Planarity : 0.004 0.030 2420 Dihedral : 4.244 16.229 1865 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.28 % Allowed : 11.81 % Favored : 85.91 % 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 aren not related in a simple way. whole: 1.58 (0.20), residues: 1680 helix: 1.76 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.51 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 126 TYR 0.030 0.002 TYR C 33 PHE 0.026 0.002 PHE E 248 TRP 0.015 0.002 TRP A 94 HIS 0.003 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00361 (14320) covalent geometry : angle 0.52506 (19550) hydrogen bonds : bond 0.05925 ( 935) hydrogen bonds : angle 4.38410 ( 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 227 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.722 Fit side-chains REVERT: A 300 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8423 (mt-10) REVERT: B 203 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8505 (t70) REVERT: B 300 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8358 (mt-10) REVERT: C 57 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7367 (pt0) REVERT: C 130 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8288 (ttp80) REVERT: C 300 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8401 (mt-10) REVERT: D 235 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8520 (m) REVERT: E 57 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7342 (pt0) REVERT: E 203 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8443 (t70) REVERT: E 300 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8415 (mt-10) outliers start: 34 outliers final: 15 residues processed: 219 average time/residue: 0.7369 time to fit residues: 175.4198 Evaluate side-chains 211 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 300 GLU 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 300 GLU 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 130 ARG Chi-restraints excluded: chain C residue 231 SER 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 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 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 Chi-restraints excluded: chain E residue 300 GLU 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: 2.9990 chunk 85 optimal weight: 0.5980 chunk 158 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 80 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 16 optimal weight: 0.0370 chunk 8 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN D 159 GLN E 11 ASN E 159 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114123 restraints weight = 14476.299| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.09 r_work: 0.3274 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14320 Z= 0.136 Angle : 0.493 6.050 19550 Z= 0.265 Chirality : 0.037 0.157 2170 Planarity : 0.004 0.030 2420 Dihedral : 4.101 15.347 1865 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.01 % Allowed : 13.29 % Favored : 84.70 % 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: 1.71 (0.20), residues: 1680 helix: 1.88 (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 0.001 0.000 ARG E 105 TYR 0.030 0.002 TYR C 33 PHE 0.023 0.002 PHE A 248 TRP 0.014 0.001 TRP A 94 HIS 0.002 0.000 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00288 (14320) covalent geometry : angle 0.49325 (19550) hydrogen bonds : bond 0.05525 ( 935) hydrogen bonds : angle 4.30977 ( 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 226 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.599 Fit side-chains REVERT: A 300 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: B 203 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8542 (t70) REVERT: B 290 VAL cc_start: 0.8644 (m) cc_final: 0.8437 (t) REVERT: C 300 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8364 (mt-10) REVERT: D 300 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8577 (mt-10) REVERT: E 300 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8346 (mt-10) outliers start: 30 outliers final: 12 residues processed: 219 average time/residue: 0.7062 time to fit residues: 168.7363 Evaluate side-chains 201 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 300 GLU 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 C residue 129 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 300 GLU 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: 2.9990 chunk 150 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 157 optimal weight: 0.0060 chunk 108 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 158 optimal weight: 0.9980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 159 GLN D 159 GLN E 159 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113484 restraints weight = 14354.036| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.09 r_work: 0.3262 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1596 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= 0.150 Angle : 0.508 6.420 19550 Z= 0.272 Chirality : 0.038 0.158 2170 Planarity : 0.004 0.030 2420 Dihedral : 4.118 15.565 1865 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.88 % Allowed : 13.42 % Favored : 84.70 % 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: 1.71 (0.20), residues: 1680 helix: 1.88 (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 E 105 TYR 0.031 0.002 TYR C 33 PHE 0.024 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 covalent geometry : bond 0.00324 (14320) covalent geometry : angle 0.50798 (19550) hydrogen bonds : bond 0.05695 ( 935) hydrogen bonds : angle 4.32342 ( 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 219 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.587 Fit side-chains REVERT: A 300 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8379 (mt-10) REVERT: B 203 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8510 (t70) REVERT: D 300 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8625 (mt-10) REVERT: E 203 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8507 (t70) REVERT: E 300 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8371 (mt-10) outliers start: 28 outliers final: 13 residues processed: 213 average time/residue: 0.6831 time to fit residues: 158.9135 Evaluate side-chains 203 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 300 GLU 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 B residue 332 MET 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 231 SER Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 336 MET 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 300 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 0.0770 chunk 4 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 chunk 112 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN 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 = 0.3708 r_free = 0.3708 target = 0.142779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.121703 restraints weight = 13760.633| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.06 r_work: 0.3373 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1610 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= 0.142 Angle : 0.501 6.099 19550 Z= 0.269 Chirality : 0.038 0.159 2170 Planarity : 0.004 0.030 2420 Dihedral : 4.073 15.284 1865 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.41 % Allowed : 14.16 % 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 aren not related in a simple way. whole: 1.74 (0.20), residues: 1680 helix: 1.91 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.51 (0.26), residues: 530 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 0.023 0.002 PHE E 248 TRP 0.014 0.001 TRP E 94 HIS 0.003 0.000 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00303 (14320) covalent geometry : angle 0.50052 (19550) hydrogen bonds : bond 0.05565 ( 935) hydrogen bonds : angle 4.30032 ( 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 213 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.621 Fit side-chains REVERT: A 300 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8367 (mt-10) REVERT: B 203 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8550 (t70) REVERT: D 300 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8563 (mt-10) REVERT: E 203 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8485 (t70) REVERT: E 300 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8337 (mt-10) outliers start: 21 outliers final: 12 residues processed: 210 average time/residue: 0.6944 time to fit residues: 159.2305 Evaluate side-chains 204 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 300 GLU 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 B residue 332 MET 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 231 SER Chi-restraints excluded: chain D residue 300 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 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 75 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 130 optimal weight: 0.0770 chunk 22 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 157 optimal weight: 0.2980 chunk 53 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 131 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN 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 = 0.3612 r_free = 0.3612 target = 0.136958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115037 restraints weight = 14396.322| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.09 r_work: 0.3283 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14320 Z= 0.134 Angle : 0.488 5.956 19550 Z= 0.262 Chirality : 0.037 0.156 2170 Planarity : 0.004 0.030 2420 Dihedral : 4.016 14.845 1865 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.41 % Allowed : 14.16 % 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 aren not related in a simple way. whole: 1.80 (0.20), residues: 1680 helix: 1.96 (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 E 105 TYR 0.032 0.002 TYR C 33 PHE 0.022 0.002 PHE E 248 TRP 0.014 0.001 TRP E 94 HIS 0.003 0.000 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00281 (14320) covalent geometry : angle 0.48833 (19550) hydrogen bonds : bond 0.05412 ( 935) hydrogen bonds : angle 4.27004 ( 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 213 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.605 Fit side-chains REVERT: A 300 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8341 (mt-10) REVERT: B 203 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8538 (t70) REVERT: B 290 VAL cc_start: 0.8636 (m) cc_final: 0.8401 (t) REVERT: D 57 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7246 (pt0) REVERT: D 300 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8561 (mt-10) REVERT: E 80 PHE cc_start: 0.7306 (t80) cc_final: 0.6921 (t80) REVERT: E 203 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8471 (t70) REVERT: E 300 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8340 (mt-10) outliers start: 21 outliers final: 10 residues processed: 211 average time/residue: 0.6832 time to fit residues: 157.4980 Evaluate side-chains 205 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 300 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP 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 231 SER Chi-restraints excluded: chain D residue 300 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 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: 5.9990 chunk 34 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 125 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 114 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 159 GLN E 159 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113860 restraints weight = 14352.049| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.09 r_work: 0.3266 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1624 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= 0.151 Angle : 0.512 6.355 19550 Z= 0.274 Chirality : 0.038 0.159 2170 Planarity : 0.004 0.029 2420 Dihedral : 4.096 15.612 1865 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.28 % Allowed : 14.36 % Favored : 84.36 % 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 (0.20), residues: 1680 helix: 1.90 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.48 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 105 TYR 0.033 0.002 TYR C 33 PHE 0.023 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 covalent geometry : bond 0.00330 (14320) covalent geometry : angle 0.51230 (19550) hydrogen bonds : bond 0.05665 ( 935) hydrogen bonds : angle 4.31070 ( 2730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5004.87 seconds wall clock time: 86 minutes 27.39 seconds (5187.39 seconds total)