Starting phenix.real_space_refine on Fri May 16 05:32:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9egt_47997/05_2025/9egt_47997.cif Found real_map, /net/cci-nas-00/data/ceres_data/9egt_47997/05_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_47997/05_2025/9egt_47997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9egt_47997/05_2025/9egt_47997.map" model { file = "/net/cci-nas-00/data/ceres_data/9egt_47997/05_2025/9egt_47997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9egt_47997/05_2025/9egt_47997.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, '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: C, B, E, D Time building chain proxies: 9.08, per 1000 atoms: 0.64 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: 3.36 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.22 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: 4.48 Time building geometry restraints manager: 4.00 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 13.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 33.590 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.490 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.012 0.001 TRP A 94 HIS 0.003 0.001 HIS E 326 PHE 0.020 0.001 PHE D 248 TYR 0.016 0.001 TYR E 97 ARG 0.002 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.13348 ( 935) hydrogen bonds : angle 5.75750 ( 2730) covalent geometry : bond 0.00225 (14320) covalent geometry : angle 0.47897 (19550) *********************** 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 : 1.750 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: 1.3296 time to fit residues: 364.6608 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 : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.135486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113534 restraints weight = 14351.006| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.09 r_work: 0.3265 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1170 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= 0.170 Angle : 0.532 6.451 19550 Z= 0.287 Chirality : 0.039 0.159 2170 Planarity : 0.005 0.031 2420 Dihedral : 4.193 16.776 1865 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.14 % Allowed : 8.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.20), residues: 1680 helix: 1.57 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.43 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 94 HIS 0.003 0.001 HIS E 326 PHE 0.025 0.002 PHE E 248 TYR 0.022 0.002 TYR D 97 ARG 0.002 0.000 ARG D 313 Details of bonding type rmsd hydrogen bonds : bond 0.06131 ( 935) hydrogen bonds : angle 4.53557 ( 2730) covalent geometry : bond 0.00372 (14320) covalent geometry : angle 0.53173 (19550) *********************** 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 224 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 1.552 Fit side-chains REVERT: D 324 GLU cc_start: 0.8478 (mp0) cc_final: 0.8239 (mp0) REVERT: E 57 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7342 (pt0) outliers start: 17 outliers final: 5 residues processed: 218 average time/residue: 1.2628 time to fit residues: 302.1928 Evaluate side-chains 205 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 199 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 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 39 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 159 GLN D 159 GLN E 11 ASN E 159 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110383 restraints weight = 14412.992| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.09 r_work: 0.3222 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1549 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= 0.209 Angle : 0.570 6.936 19550 Z= 0.305 Chirality : 0.041 0.163 2170 Planarity : 0.005 0.033 2420 Dihedral : 4.392 17.063 1865 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.62 % Allowed : 9.33 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.20), residues: 1680 helix: 1.57 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.43 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 94 HIS 0.004 0.001 HIS E 326 PHE 0.029 0.002 PHE E 248 TYR 0.027 0.002 TYR C 97 ARG 0.003 0.000 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.06506 ( 935) hydrogen bonds : angle 4.53693 ( 2730) covalent geometry : bond 0.00478 (14320) covalent geometry : angle 0.57023 (19550) *********************** 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 230 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 1.489 Fit side-chains REVERT: B 130 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8541 (ttp80) REVERT: E 203 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8472 (t70) outliers start: 39 outliers final: 16 residues processed: 224 average time/residue: 1.2712 time to fit residues: 311.9503 Evaluate side-chains 205 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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 130 ARG Chi-restraints excluded: chain B residue 271 LEU 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 175 SER Chi-restraints excluded: chain D residue 203 ASP 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 122 optimal weight: 0.9990 chunk 49 optimal weight: 0.0770 chunk 56 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 145 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.135685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113753 restraints weight = 14317.814| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.09 r_work: 0.3269 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14320 Z= 0.142 Angle : 0.504 6.070 19550 Z= 0.273 Chirality : 0.038 0.157 2170 Planarity : 0.004 0.028 2420 Dihedral : 4.159 15.752 1865 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.08 % Allowed : 10.47 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.20), residues: 1680 helix: 1.78 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.42 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 94 HIS 0.002 0.000 HIS E 326 PHE 0.025 0.002 PHE A 248 TYR 0.027 0.002 TYR C 33 ARG 0.002 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.05699 ( 935) hydrogen bonds : angle 4.35757 ( 2730) covalent geometry : bond 0.00302 (14320) covalent geometry : angle 0.50420 (19550) *********************** 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 223 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 1.600 Fit side-chains REVERT: A 300 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8383 (mt-10) REVERT: B 57 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7314 (pt0) REVERT: D 57 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7231 (pt0) REVERT: E 57 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7216 (pt0) REVERT: E 203 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8439 (t70) REVERT: E 300 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8366 (mt-10) outliers start: 31 outliers final: 11 residues processed: 214 average time/residue: 1.3485 time to fit residues: 315.2474 Evaluate side-chains 199 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 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 57 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 175 SER 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 300 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 147 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.132839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110763 restraints weight = 14464.476| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.09 r_work: 0.3227 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 14320 Z= 0.198 Angle : 0.561 6.905 19550 Z= 0.300 Chirality : 0.040 0.164 2170 Planarity : 0.005 0.029 2420 Dihedral : 4.342 16.766 1865 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.75 % Allowed : 11.28 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.20), residues: 1680 helix: 1.73 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.43 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 94 HIS 0.003 0.001 HIS E 326 PHE 0.028 0.002 PHE E 248 TYR 0.029 0.002 TYR C 33 ARG 0.003 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.06319 ( 935) hydrogen bonds : angle 4.44471 ( 2730) covalent geometry : bond 0.00453 (14320) covalent geometry : angle 0.56093 (19550) *********************** 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 226 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 1.468 Fit side-chains REVERT: A 300 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8453 (mt-10) REVERT: C 57 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7391 (pt0) REVERT: D 300 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8635 (mt-10) REVERT: E 203 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8443 (t70) REVERT: E 300 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8444 (mt-10) outliers start: 41 outliers final: 19 residues processed: 214 average time/residue: 1.3687 time to fit residues: 321.6605 Evaluate side-chains 206 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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 57 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 332 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 D residue 57 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 300 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 126 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 164 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.134483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112473 restraints weight = 14554.495| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.10 r_work: 0.3250 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 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 : 0.004 0.033 14320 Z= 0.160 Angle : 0.519 6.298 19550 Z= 0.280 Chirality : 0.039 0.159 2170 Planarity : 0.004 0.029 2420 Dihedral : 4.219 16.414 1865 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.35 % Allowed : 12.08 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.20), residues: 1680 helix: 1.80 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.48 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 94 HIS 0.003 0.001 HIS E 326 PHE 0.026 0.002 PHE E 248 TYR 0.029 0.002 TYR C 33 ARG 0.002 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.05877 ( 935) hydrogen bonds : angle 4.36723 ( 2730) covalent geometry : bond 0.00352 (14320) covalent geometry : angle 0.51949 (19550) *********************** 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 223 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 1.676 Fit side-chains REVERT: A 300 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8418 (mt-10) REVERT: C 130 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8293 (ttp80) REVERT: D 235 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8516 (m) REVERT: D 300 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8602 (mt-10) REVERT: E 57 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7342 (pt0) REVERT: E 203 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8444 (t70) REVERT: E 300 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8409 (mt-10) outliers start: 35 outliers final: 16 residues processed: 213 average time/residue: 1.3131 time to fit residues: 305.6906 Evaluate side-chains 203 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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 332 MET Chi-restraints excluded: chain B residue 336 MET 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 175 SER 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 300 GLU 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 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 98 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 70 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.133968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111973 restraints weight = 14500.982| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.09 r_work: 0.3242 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14320 Z= 0.170 Angle : 0.530 6.574 19550 Z= 0.284 Chirality : 0.039 0.160 2170 Planarity : 0.004 0.030 2420 Dihedral : 4.245 16.428 1865 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.48 % Allowed : 12.75 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.20), residues: 1680 helix: 1.80 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.49 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 94 HIS 0.003 0.001 HIS E 326 PHE 0.026 0.002 PHE E 248 TYR 0.030 0.002 TYR C 33 ARG 0.002 0.000 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.05977 ( 935) hydrogen bonds : angle 4.38251 ( 2730) covalent geometry : bond 0.00378 (14320) covalent geometry : angle 0.53039 (19550) *********************** 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: 37 poor density : 184 time to evaluate : 1.549 Fit side-chains REVERT: A 300 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8424 (mt-10) REVERT: B 203 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8499 (t70) REVERT: C 130 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8300 (ttp80) REVERT: D 300 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8604 (mt-10) REVERT: E 203 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8445 (t70) REVERT: E 300 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8407 (mt-10) outliers start: 37 outliers final: 15 residues processed: 213 average time/residue: 1.3530 time to fit residues: 313.9240 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 : 1.508 ------------------------------------------------------------------------------- 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 332 MET 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 175 SER Chi-restraints excluded: chain D residue 203 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.135710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113376 restraints weight = 14475.445| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.14 r_work: 0.3272 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1576 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= 0.147 Angle : 0.505 6.158 19550 Z= 0.271 Chirality : 0.038 0.158 2170 Planarity : 0.004 0.029 2420 Dihedral : 4.133 15.605 1865 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.74 % Allowed : 13.49 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.20), residues: 1680 helix: 1.86 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.47 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 94 HIS 0.003 0.000 HIS E 326 PHE 0.024 0.002 PHE A 248 TYR 0.031 0.002 TYR C 33 ARG 0.002 0.000 ARG E 105 Details of bonding type rmsd hydrogen bonds : bond 0.05659 ( 935) hydrogen bonds : angle 4.32903 ( 2730) covalent geometry : bond 0.00316 (14320) covalent geometry : angle 0.50493 (19550) *********************** 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 213 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 1.537 Fit side-chains REVERT: A 300 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8381 (mt-10) REVERT: B 203 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8523 (t70) REVERT: B 290 VAL cc_start: 0.8631 (m) cc_final: 0.8396 (t) REVERT: D 300 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8582 (mt-10) REVERT: E 203 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8426 (t70) REVERT: E 300 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8387 (mt-10) outliers start: 26 outliers final: 15 residues processed: 207 average time/residue: 1.2860 time to fit residues: 291.5650 Evaluate side-chains 203 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 B residue 332 MET Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 203 ASP 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 62 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 142 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.135303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113325 restraints weight = 14364.844| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.09 r_work: 0.3258 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1609 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= 0.152 Angle : 0.512 6.258 19550 Z= 0.275 Chirality : 0.038 0.158 2170 Planarity : 0.004 0.030 2420 Dihedral : 4.135 15.666 1865 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.61 % Allowed : 13.83 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.20), residues: 1680 helix: 1.87 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.47 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 94 HIS 0.003 0.000 HIS E 326 PHE 0.024 0.002 PHE E 248 TYR 0.032 0.002 TYR C 33 ARG 0.002 0.000 ARG E 105 Details of bonding type rmsd hydrogen bonds : bond 0.05716 ( 935) hydrogen bonds : angle 4.33541 ( 2730) covalent geometry : bond 0.00331 (14320) covalent geometry : angle 0.51227 (19550) *********************** 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 214 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 1.521 Fit side-chains REVERT: A 300 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8392 (mt-10) REVERT: B 203 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8506 (t70) REVERT: E 203 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8431 (t70) REVERT: E 300 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8383 (mt-10) outliers start: 24 outliers final: 13 residues processed: 209 average time/residue: 1.2318 time to fit residues: 282.9871 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 : 1.486 ------------------------------------------------------------------------------- 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 B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP 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 129 ILE Chi-restraints excluded: chain D residue 175 SER 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 300 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 47 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 124 optimal weight: 0.3980 chunk 112 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.136106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114180 restraints weight = 14438.800| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.09 r_work: 0.3271 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14320 Z= 0.145 Angle : 0.505 6.115 19550 Z= 0.271 Chirality : 0.038 0.159 2170 Planarity : 0.004 0.030 2420 Dihedral : 4.096 15.345 1865 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.21 % Allowed : 14.23 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.20), residues: 1680 helix: 1.89 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.47 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 94 HIS 0.003 0.000 HIS E 326 PHE 0.024 0.002 PHE A 248 TYR 0.032 0.002 TYR C 33 ARG 0.002 0.000 ARG E 105 Details of bonding type rmsd hydrogen bonds : bond 0.05601 ( 935) hydrogen bonds : angle 4.31174 ( 2730) covalent geometry : bond 0.00311 (14320) covalent geometry : angle 0.50517 (19550) ********************** 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 206 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 1.662 Fit side-chains REVERT: A 300 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: B 203 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8508 (t70) REVERT: D 300 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8552 (mt-10) REVERT: E 203 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8419 (t70) REVERT: E 300 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8380 (mt-10) outliers start: 18 outliers final: 12 residues processed: 204 average time/residue: 1.2669 time to fit residues: 283.6781 Evaluate side-chains 203 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 1.452 ------------------------------------------------------------------------------- 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 332 MET Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 203 ASP 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 159 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 160 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 97 optimal weight: 0.0970 chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 C 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 = 0.3597 r_free = 0.3597 target = 0.135550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113616 restraints weight = 14413.452| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.09 r_work: 0.3263 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1615 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= 0.152 Angle : 0.513 6.233 19550 Z= 0.275 Chirality : 0.038 0.158 2170 Planarity : 0.004 0.030 2420 Dihedral : 4.121 15.595 1865 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.34 % Allowed : 14.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.20), residues: 1680 helix: 1.87 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.47 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 94 HIS 0.003 0.000 HIS E 326 PHE 0.028 0.002 PHE E 80 TYR 0.033 0.002 TYR C 33 ARG 0.002 0.000 ARG E 105 Details of bonding type rmsd hydrogen bonds : bond 0.05695 ( 935) hydrogen bonds : angle 4.32671 ( 2730) covalent geometry : bond 0.00332 (14320) covalent geometry : angle 0.51319 (19550) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9482.05 seconds wall clock time: 165 minutes 10.59 seconds (9910.59 seconds total)