Starting phenix.real_space_refine on Thu Jul 2 23:21:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pqj_71784/07_2026/9pqj_71784.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pqj_71784/07_2026/9pqj_71784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pqj_71784/07_2026/9pqj_71784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pqj_71784/07_2026/9pqj_71784.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pqj_71784/07_2026/9pqj_71784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pqj_71784/07_2026/9pqj_71784.map" } resolution = 2.36 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 36 5.16 5 C 6756 2.51 5 N 1758 2.21 5 O 1983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10557 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "B" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "C" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "D" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "F" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 2.72, per 1000 atoms: 0.26 Number of scatterers: 10557 At special positions: 0 Unit cell: (111.72, 116.76, 85.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 18 15.00 Mg 6 11.99 O 1983 8.00 N 1758 7.00 C 6756 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: 1.09 Conformation dependent library (CDL) restraints added in 362.7 milliseconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 22 sheets defined 46.6% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 133 through 140 Processing helix chain 'A' and resid 144 through 162 Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.690A pdb=" N ASN A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.529A pdb=" N ARG A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 285 through 293 removed outlier: 3.511A pdb=" N LEU A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 323 Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 133 through 140 Processing helix chain 'B' and resid 144 through 162 Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 232 through 238 removed outlier: 3.531A pdb=" N ARG B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 Processing helix chain 'B' and resid 285 through 293 Processing helix chain 'B' and resid 307 through 323 Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 133 through 140 Processing helix chain 'C' and resid 144 through 162 Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.687A pdb=" N ASN C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 232 through 238 removed outlier: 3.545A pdb=" N ARG C 236 " --> pdb=" O SER C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 Processing helix chain 'C' and resid 285 through 293 Processing helix chain 'C' and resid 307 through 323 Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 133 through 140 Processing helix chain 'D' and resid 144 through 162 Processing helix chain 'D' and resid 182 through 195 Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 232 through 238 removed outlier: 3.554A pdb=" N ARG D 236 " --> pdb=" O SER D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 removed outlier: 3.699A pdb=" N PHE D 271 " --> pdb=" O PRO D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 293 removed outlier: 3.502A pdb=" N LEU D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 323 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 133 through 140 Processing helix chain 'E' and resid 144 through 161 Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 232 through 239 removed outlier: 3.509A pdb=" N ARG E 236 " --> pdb=" O SER E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 271 Processing helix chain 'E' and resid 285 through 293 Processing helix chain 'E' and resid 307 through 323 Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 133 through 140 Processing helix chain 'F' and resid 144 through 161 Processing helix chain 'F' and resid 182 through 195 Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 232 through 238 removed outlier: 3.531A pdb=" N ARG F 236 " --> pdb=" O SER F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 271 Processing helix chain 'F' and resid 285 through 293 Processing helix chain 'F' and resid 307 through 323 Processing sheet with id=AA1, first strand: chain 'A' and resid 199 through 201 removed outlier: 6.465A pdb=" N TRP A 200 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASP A 221 " --> pdb=" O TRP A 200 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 177 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N TYR A 302 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP A 174 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N PHE A 304 " --> pdb=" O TRP A 174 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS A 176 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 244 through 247 Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 274 Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 201 removed outlier: 6.555A pdb=" N TRP B 200 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 177 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N TYR B 302 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TRP B 174 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE B 304 " --> pdb=" O TRP B 174 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS B 176 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 244 through 247 Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 274 Processing sheet with id=AA8, first strand: chain 'B' and resid 294 through 295 Processing sheet with id=AA9, first strand: chain 'C' and resid 199 through 201 removed outlier: 6.523A pdb=" N TRP C 200 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY C 177 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N TYR C 302 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP C 174 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE C 304 " --> pdb=" O TRP C 174 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS C 176 " --> pdb=" O PHE C 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 244 through 247 Processing sheet with id=AB2, first strand: chain 'C' and resid 273 through 274 Processing sheet with id=AB3, first strand: chain 'C' and resid 294 through 295 Processing sheet with id=AB4, first strand: chain 'D' and resid 199 through 201 removed outlier: 6.417A pdb=" N TRP D 200 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY D 177 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N TYR D 302 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TRP D 174 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE D 304 " --> pdb=" O TRP D 174 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS D 176 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 244 through 247 Processing sheet with id=AB6, first strand: chain 'D' and resid 273 through 274 Processing sheet with id=AB7, first strand: chain 'E' and resid 199 through 201 removed outlier: 6.494A pdb=" N TRP E 200 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY E 177 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N TYR E 302 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TRP E 174 " --> pdb=" O TYR E 302 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N PHE E 304 " --> pdb=" O TRP E 174 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS E 176 " --> pdb=" O PHE E 304 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 244 through 247 Processing sheet with id=AB9, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AC1, first strand: chain 'F' and resid 199 through 201 removed outlier: 6.496A pdb=" N TRP F 200 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY F 177 " --> pdb=" O SER F 263 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N TYR F 302 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TRP F 174 " --> pdb=" O TYR F 302 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N PHE F 304 " --> pdb=" O TRP F 174 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS F 176 " --> pdb=" O PHE F 304 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 244 through 247 Processing sheet with id=AC3, first strand: chain 'F' and resid 273 through 274 Processing sheet with id=AC4, first strand: chain 'F' and resid 294 through 295 456 hydrogen bonds defined for protein. 1284 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: 1.21 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: 1.21 - 1.36: 3336 1.36 - 1.50: 3046 1.50 - 1.65: 4310 1.65 - 1.80: 33 1.80 - 1.95: 33 Bond restraints: 10758 Sorted by residual: bond pdb=" O3B AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sigma weight residual 1.673 1.577 0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" O3B AGS A 402 " pdb=" PB AGS A 402 " ideal model delta sigma weight residual 1.673 1.577 0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" O3B AGS E 402 " pdb=" PB AGS E 402 " ideal model delta sigma weight residual 1.673 1.578 0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" O3B AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sigma weight residual 1.673 1.578 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" O3B AGS C 401 " pdb=" PB AGS C 401 " ideal model delta sigma weight residual 1.673 1.578 0.095 2.00e-02 2.50e+03 2.24e+01 ... (remaining 10753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 14260 2.01 - 4.02: 242 4.02 - 6.03: 25 6.03 - 8.05: 22 8.05 - 10.06: 13 Bond angle restraints: 14562 Sorted by residual: angle pdb=" O1B AGS C 401 " pdb=" PB AGS C 401 " pdb=" O2B AGS C 401 " ideal model delta sigma weight residual 121.53 111.47 10.06 3.00e+00 1.11e-01 1.12e+01 angle pdb=" O1A AGS B 401 " pdb=" PA AGS B 401 " pdb=" O2A AGS B 401 " ideal model delta sigma weight residual 122.09 112.10 9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" O1A AGS C 402 " pdb=" PA AGS C 402 " pdb=" O2A AGS C 402 " ideal model delta sigma weight residual 122.09 112.26 9.83 3.00e+00 1.11e-01 1.07e+01 angle pdb=" O1A AGS A 402 " pdb=" PA AGS A 402 " pdb=" O2A AGS A 402 " ideal model delta sigma weight residual 122.09 112.31 9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" O1A AGS E 401 " pdb=" PA AGS E 401 " pdb=" O2A AGS E 401 " ideal model delta sigma weight residual 122.09 112.31 9.78 3.00e+00 1.11e-01 1.06e+01 ... (remaining 14557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.34: 5873 18.34 - 36.69: 411 36.69 - 55.03: 101 55.03 - 73.38: 82 73.38 - 91.72: 61 Dihedral angle restraints: 6528 sinusoidal: 2934 harmonic: 3594 Sorted by residual: dihedral pdb=" O1A AGS B 401 " pdb=" O3A AGS B 401 " pdb=" PA AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sinusoidal sigma weight residual 82.37 -9.35 91.72 1 3.00e+01 1.11e-03 1.10e+01 dihedral pdb=" CA GLN B 246 " pdb=" C GLN B 246 " pdb=" N VAL B 247 " pdb=" CA VAL B 247 " ideal model delta harmonic sigma weight residual 180.00 163.57 16.43 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" O1A AGS C 401 " pdb=" O3A AGS C 401 " pdb=" PA AGS C 401 " pdb=" PB AGS C 401 " ideal model delta sinusoidal sigma weight residual 82.37 -7.89 90.26 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 6525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1265 0.057 - 0.114: 242 0.114 - 0.171: 10 0.171 - 0.228: 1 0.228 - 0.285: 6 Chirality restraints: 1524 Sorted by residual: chirality pdb=" C3' AGS C 401 " pdb=" C2' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" O3' AGS C 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.66 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C3' AGS B 401 " pdb=" C2' AGS B 401 " pdb=" C4' AGS B 401 " pdb=" O3' AGS B 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C3' AGS E 402 " pdb=" C2' AGS E 402 " pdb=" C4' AGS E 402 " pdb=" O3' AGS E 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1521 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 203 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.56e+00 pdb=" CG ASN F 203 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN F 203 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN F 203 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 255 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO B 256 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 256 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 256 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 255 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO E 256 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO E 256 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 256 " 0.016 5.00e-02 4.00e+02 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 70 2.49 - 3.09: 6986 3.09 - 3.70: 15619 3.70 - 4.30: 25375 4.30 - 4.90: 39841 Nonbonded interactions: 87891 Sorted by model distance: nonbonded pdb="MG MG C 403 " pdb=" O HOH C 503 " model vdw 1.891 2.170 nonbonded pdb="MG MG A 401 " pdb=" O2B AGS B 401 " model vdw 1.901 2.170 nonbonded pdb=" O2B AGS C 402 " pdb="MG MG C 403 " model vdw 1.908 2.170 nonbonded pdb="MG MG B 402 " pdb=" O2B AGS C 401 " model vdw 1.918 2.170 nonbonded pdb="MG MG A 401 " pdb=" O HOH A 503 " model vdw 1.928 2.170 ... (remaining 87886 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 121 through 327) selection = (chain 'B' and resid 121 through 327) selection = (chain 'C' and resid 121 through 327) selection = (chain 'D' and resid 121 through 327) selection = (chain 'E' and resid 121 through 327) selection = (chain 'F' and resid 121 through 327) } 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.340 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 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 : 0.006 0.096 10758 Z= 0.281 Angle : 0.710 10.056 14562 Z= 0.334 Chirality : 0.047 0.285 1524 Planarity : 0.004 0.039 1818 Dihedral : 17.952 91.720 4212 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.24), residues: 1230 helix: 1.12 (0.22), residues: 540 sheet: 1.69 (0.48), residues: 114 loop : 0.38 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 224 TYR 0.016 0.002 TYR E 212 PHE 0.009 0.001 PHE E 223 TRP 0.013 0.002 TRP B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.28 (10758) covalent geometry : angle 0.71005 / 0.33 (14562) hydrogen bonds : bond 0.14113 / 9.39 ( 456) hydrogen bonds : angle 6.36445 / 4.64 ( 1284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 123 ARG cc_start: 0.7468 (mtp85) cc_final: 0.7072 (mtt90) REVERT: A 166 LYS cc_start: 0.8584 (mttm) cc_final: 0.8282 (mptt) REVERT: A 198 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7931 (tt0) REVERT: A 222 ASP cc_start: 0.8631 (t70) cc_final: 0.8391 (t70) REVERT: A 230 GLU cc_start: 0.8398 (pt0) cc_final: 0.7325 (tp30) REVERT: A 297 ASP cc_start: 0.8328 (m-30) cc_final: 0.8118 (m-30) REVERT: A 298 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7226 (mm-30) REVERT: A 320 LYS cc_start: 0.8371 (tttt) cc_final: 0.8019 (ttpm) REVERT: B 123 ARG cc_start: 0.7752 (mtp85) cc_final: 0.7535 (mtt-85) REVERT: B 140 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7863 (mt-10) REVERT: B 230 GLU cc_start: 0.8649 (pt0) cc_final: 0.8238 (pm20) REVERT: B 298 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7915 (mm-30) REVERT: B 320 LYS cc_start: 0.8608 (tttt) cc_final: 0.8320 (ttpt) REVERT: B 327 MET cc_start: 0.7157 (mtp) cc_final: 0.6888 (mtp) REVERT: C 124 GLU cc_start: 0.7969 (tt0) cc_final: 0.7688 (pt0) REVERT: C 140 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7698 (mp0) REVERT: C 165 ASP cc_start: 0.7870 (m-30) cc_final: 0.7470 (p0) REVERT: C 196 ASN cc_start: 0.8514 (t0) cc_final: 0.8130 (m110) REVERT: C 198 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8092 (mm-30) REVERT: C 296 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8228 (mt-10) REVERT: C 298 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7685 (mm-30) REVERT: D 140 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7824 (mm-30) REVERT: D 222 ASP cc_start: 0.8596 (t70) cc_final: 0.8150 (t70) REVERT: D 230 GLU cc_start: 0.8684 (pt0) cc_final: 0.7923 (tp30) REVERT: D 309 GLN cc_start: 0.7698 (mt0) cc_final: 0.7267 (pm20) REVERT: E 123 ARG cc_start: 0.7906 (mtp85) cc_final: 0.7626 (mtp85) REVERT: E 165 ASP cc_start: 0.8216 (m-30) cc_final: 0.7976 (t0) REVERT: E 281 ILE cc_start: 0.8149 (mp) cc_final: 0.7838 (mm) REVERT: E 309 GLN cc_start: 0.7855 (mt0) cc_final: 0.7648 (pm20) REVERT: E 320 LYS cc_start: 0.8681 (tttt) cc_final: 0.8316 (ttpp) REVERT: F 122 LYS cc_start: 0.7956 (mttt) cc_final: 0.7671 (mttp) REVERT: F 298 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7773 (mm-30) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.6514 time to fit residues: 201.8885 Evaluate side-chains 216 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 ASN A 246 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN C 255 GLN C 272 GLN C 311 GLN D 131 ASN D 246 GLN D 311 GLN E 159 GLN E 161 GLN E 168 GLN E 272 GLN E 303 ASN F 246 GLN F 272 GLN F 288 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.087128 restraints weight = 11323.398| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.03 r_work: 0.2794 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10758 Z= 0.184 Angle : 0.553 6.600 14562 Z= 0.289 Chirality : 0.043 0.131 1524 Planarity : 0.004 0.039 1818 Dihedral : 12.589 50.405 1572 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.11 % Allowed : 8.61 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.24), residues: 1230 helix: 1.08 (0.22), residues: 540 sheet: 0.05 (0.37), residues: 174 loop : 0.57 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.017 0.002 TYR A 212 PHE 0.009 0.001 PHE E 223 TRP 0.024 0.002 TRP A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (10758) covalent geometry : angle 0.55259 / 0.29 (14562) hydrogen bonds : bond 0.05762 / 3.79 ( 456) hydrogen bonds : angle 5.09940 / 3.69 ( 1284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8052 (tt0) REVERT: A 230 GLU cc_start: 0.8236 (pt0) cc_final: 0.7525 (tp30) REVERT: A 298 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7442 (mm-30) REVERT: A 319 ARG cc_start: 0.8439 (mtt-85) cc_final: 0.8138 (mtt-85) REVERT: A 320 LYS cc_start: 0.8619 (tttt) cc_final: 0.8294 (ttpm) REVERT: B 136 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: B 198 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7904 (mm-30) REVERT: B 230 GLU cc_start: 0.8547 (pt0) cc_final: 0.8118 (pm20) REVERT: B 298 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7843 (mm-30) REVERT: B 320 LYS cc_start: 0.8553 (tttt) cc_final: 0.8243 (ttpt) REVERT: C 196 ASN cc_start: 0.8471 (t0) cc_final: 0.8117 (m110) REVERT: C 198 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8251 (mt-10) REVERT: C 296 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8228 (mt-10) REVERT: C 298 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7750 (mm-30) REVERT: D 140 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7839 (mm-30) REVERT: D 309 GLN cc_start: 0.7874 (mt0) cc_final: 0.7427 (pm20) REVERT: E 123 ARG cc_start: 0.7823 (mtp85) cc_final: 0.7528 (mtp85) REVERT: E 165 ASP cc_start: 0.8305 (m-30) cc_final: 0.7966 (t0) REVERT: E 213 ARG cc_start: 0.8627 (mtm-85) cc_final: 0.8216 (mtm-85) REVERT: E 288 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.7992 (mt0) REVERT: E 315 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: F 122 LYS cc_start: 0.7933 (mttt) cc_final: 0.7538 (mttp) REVERT: F 127 GLU cc_start: 0.8253 (tt0) cc_final: 0.7765 (tm-30) REVERT: F 135 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7095 (tmt170) REVERT: F 178 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8533 (mm-30) REVERT: F 298 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7544 (mm-30) outliers start: 23 outliers final: 6 residues processed: 222 average time/residue: 0.5477 time to fit residues: 129.5393 Evaluate side-chains 206 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 315 GLU Chi-restraints excluded: chain F residue 135 ARG Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 310 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 78 optimal weight: 0.0070 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 114 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN B 246 GLN C 246 GLN C 311 GLN D 156 ASN D 196 ASN D 246 GLN D 311 GLN E 303 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.090687 restraints weight = 11265.736| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.03 r_work: 0.2857 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10758 Z= 0.101 Angle : 0.436 4.462 14562 Z= 0.235 Chirality : 0.040 0.129 1524 Planarity : 0.003 0.029 1818 Dihedral : 7.296 31.369 1572 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.83 % Allowed : 10.44 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.24), residues: 1230 helix: 1.32 (0.22), residues: 540 sheet: -0.02 (0.36), residues: 174 loop : 0.71 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.008 0.001 TYR B 295 PHE 0.005 0.001 PHE E 271 TRP 0.024 0.001 TRP B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (10758) covalent geometry : angle 0.43623 / 0.23 (14562) hydrogen bonds : bond 0.04219 / 2.77 ( 456) hydrogen bonds : angle 4.79833 / 3.47 ( 1284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.8234 (pt0) cc_final: 0.7533 (tp30) REVERT: A 298 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7480 (mm-30) REVERT: A 319 ARG cc_start: 0.8433 (mtt-85) cc_final: 0.8134 (mtt-85) REVERT: A 320 LYS cc_start: 0.8609 (tttt) cc_final: 0.8329 (ttpm) REVERT: B 136 GLU cc_start: 0.7655 (tt0) cc_final: 0.7317 (tt0) REVERT: B 198 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: B 230 GLU cc_start: 0.8524 (pt0) cc_final: 0.8109 (pm20) REVERT: B 298 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7844 (mm-30) REVERT: B 320 LYS cc_start: 0.8541 (tttt) cc_final: 0.8188 (ttpt) REVERT: C 196 ASN cc_start: 0.8451 (t0) cc_final: 0.8201 (m110) REVERT: C 198 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8166 (mm-30) REVERT: C 296 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8170 (mt-10) REVERT: C 298 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7778 (mm-30) REVERT: D 140 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7742 (mm-30) REVERT: D 272 GLN cc_start: 0.8016 (mt0) cc_final: 0.7709 (pt0) REVERT: D 309 GLN cc_start: 0.7862 (mt0) cc_final: 0.7408 (pm20) REVERT: E 123 ARG cc_start: 0.7800 (mtp85) cc_final: 0.7438 (mtt180) REVERT: E 140 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: E 165 ASP cc_start: 0.8267 (m-30) cc_final: 0.7912 (t0) REVERT: E 288 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7754 (mt0) REVERT: E 315 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: E 320 LYS cc_start: 0.8639 (tttt) cc_final: 0.8315 (ttpp) REVERT: F 122 LYS cc_start: 0.7913 (mttt) cc_final: 0.7508 (mttp) REVERT: F 127 GLU cc_start: 0.8238 (tt0) cc_final: 0.7756 (tm-30) REVERT: F 178 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8499 (mm-30) REVERT: F 189 ASP cc_start: 0.8576 (t70) cc_final: 0.8246 (t0) REVERT: F 298 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7484 (mm-30) outliers start: 20 outliers final: 4 residues processed: 225 average time/residue: 0.5295 time to fit residues: 126.9521 Evaluate side-chains 210 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 201 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 315 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 310 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 99 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 68 optimal weight: 0.0470 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 246 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN C 246 GLN C 255 GLN C 272 GLN C 311 GLN D 156 ASN D 196 ASN D 246 GLN D 311 GLN E 303 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.088647 restraints weight = 11242.435| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.02 r_work: 0.2827 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10758 Z= 0.131 Angle : 0.461 4.063 14562 Z= 0.249 Chirality : 0.041 0.128 1524 Planarity : 0.003 0.029 1818 Dihedral : 7.320 33.710 1572 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.20 % Allowed : 11.45 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.24), residues: 1230 helix: 1.26 (0.22), residues: 540 sheet: -0.09 (0.36), residues: 174 loop : 0.70 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.012 0.001 TYR A 212 PHE 0.008 0.001 PHE A 271 TRP 0.025 0.001 TRP B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10758) covalent geometry : angle 0.46124 / 0.25 (14562) hydrogen bonds : bond 0.04883 / 3.21 ( 456) hydrogen bonds : angle 4.79334 / 3.47 ( 1284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.8225 (pt0) cc_final: 0.7542 (tp30) REVERT: A 298 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7425 (mm-30) REVERT: A 319 ARG cc_start: 0.8470 (mtt-85) cc_final: 0.8162 (mtt-85) REVERT: A 320 LYS cc_start: 0.8620 (tttt) cc_final: 0.8369 (ttpm) REVERT: B 136 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7387 (tt0) REVERT: B 198 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7876 (mm-30) REVERT: B 230 GLU cc_start: 0.8552 (pt0) cc_final: 0.8110 (pm20) REVERT: B 298 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7841 (mm-30) REVERT: B 320 LYS cc_start: 0.8550 (tttt) cc_final: 0.8222 (ttpt) REVERT: C 140 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: C 196 ASN cc_start: 0.8522 (t0) cc_final: 0.8228 (m110) REVERT: C 198 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8181 (mm-30) REVERT: C 296 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8178 (mt-10) REVERT: C 298 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7762 (mm-30) REVERT: D 140 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7748 (mm-30) REVERT: D 272 GLN cc_start: 0.8036 (mt0) cc_final: 0.7680 (pt0) REVERT: D 309 GLN cc_start: 0.7865 (mt0) cc_final: 0.7424 (pm20) REVERT: E 123 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7394 (mtt-85) REVERT: E 140 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: E 165 ASP cc_start: 0.8277 (m-30) cc_final: 0.7958 (t0) REVERT: E 288 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7903 (mt0) REVERT: E 315 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: F 122 LYS cc_start: 0.7924 (mttt) cc_final: 0.7508 (mttp) REVERT: F 135 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7017 (tmt170) REVERT: F 189 ASP cc_start: 0.8551 (t70) cc_final: 0.8228 (t0) REVERT: F 298 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7639 (mm-30) outliers start: 24 outliers final: 8 residues processed: 216 average time/residue: 0.6093 time to fit residues: 139.7859 Evaluate side-chains 212 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 315 GLU Chi-restraints excluded: chain F residue 135 ARG Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 310 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 82 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 246 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN C 255 GLN C 272 GLN C 311 GLN D 156 ASN D 196 ASN D 246 GLN D 311 GLN E 303 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.087166 restraints weight = 11327.054| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.03 r_work: 0.2797 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10758 Z= 0.179 Angle : 0.513 4.742 14562 Z= 0.274 Chirality : 0.043 0.148 1524 Planarity : 0.004 0.036 1818 Dihedral : 8.176 41.860 1572 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.20 % Allowed : 12.73 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.24), residues: 1230 helix: 1.09 (0.22), residues: 540 sheet: -0.13 (0.36), residues: 174 loop : 0.64 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 291 TYR 0.017 0.002 TYR E 212 PHE 0.010 0.001 PHE A 271 TRP 0.032 0.002 TRP B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (10758) covalent geometry : angle 0.51286 / 0.27 (14562) hydrogen bonds : bond 0.05577 / 3.67 ( 456) hydrogen bonds : angle 4.88462 / 3.53 ( 1284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.8242 (pt0) cc_final: 0.7555 (tp30) REVERT: A 298 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7405 (mm-30) REVERT: A 320 LYS cc_start: 0.8612 (tttt) cc_final: 0.8362 (ttpm) REVERT: B 136 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: B 198 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7913 (mm-30) REVERT: B 230 GLU cc_start: 0.8579 (pt0) cc_final: 0.8113 (pm20) REVERT: B 298 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7699 (mm-30) REVERT: B 320 LYS cc_start: 0.8536 (tttt) cc_final: 0.8230 (ttpt) REVERT: C 140 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: C 196 ASN cc_start: 0.8496 (t0) cc_final: 0.8120 (m110) REVERT: C 198 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8291 (mt-10) REVERT: C 298 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7753 (mm-30) REVERT: D 140 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7810 (mm-30) REVERT: D 222 ASP cc_start: 0.8639 (t0) cc_final: 0.8215 (t70) REVERT: D 309 GLN cc_start: 0.7885 (mt0) cc_final: 0.7460 (pm20) REVERT: E 123 ARG cc_start: 0.7846 (mtp85) cc_final: 0.7510 (mtp85) REVERT: E 140 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: E 165 ASP cc_start: 0.8289 (m-30) cc_final: 0.7959 (t0) REVERT: E 288 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.7995 (mt0) REVERT: E 315 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: E 320 LYS cc_start: 0.8634 (ttpp) cc_final: 0.8294 (ttpt) REVERT: F 122 LYS cc_start: 0.7948 (mttt) cc_final: 0.7531 (mttp) REVERT: F 135 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7070 (tmt170) REVERT: F 298 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7562 (mm-30) outliers start: 24 outliers final: 7 residues processed: 213 average time/residue: 0.5468 time to fit residues: 124.1655 Evaluate side-chains 210 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 315 GLU Chi-restraints excluded: chain F residue 135 ARG Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 310 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 24 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN D 196 ASN D 246 GLN D 311 GLN E 303 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.087953 restraints weight = 11300.951| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.03 r_work: 0.2817 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10758 Z= 0.142 Angle : 0.474 5.439 14562 Z= 0.255 Chirality : 0.042 0.135 1524 Planarity : 0.004 0.029 1818 Dihedral : 7.554 37.682 1572 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.11 % Allowed : 13.92 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.24), residues: 1230 helix: 1.15 (0.22), residues: 540 sheet: -0.16 (0.36), residues: 174 loop : 0.68 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 319 TYR 0.014 0.001 TYR E 212 PHE 0.008 0.001 PHE E 271 TRP 0.037 0.001 TRP B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10758) covalent geometry : angle 0.47418 / 0.26 (14562) hydrogen bonds : bond 0.04984 / 3.28 ( 456) hydrogen bonds : angle 4.81116 / 3.48 ( 1284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.8255 (pt0) cc_final: 0.7571 (tp30) REVERT: A 281 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7563 (pp) REVERT: A 298 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7400 (mm-30) REVERT: A 320 LYS cc_start: 0.8624 (tttt) cc_final: 0.8379 (ttpm) REVERT: B 136 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: B 198 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7903 (mm-30) REVERT: B 230 GLU cc_start: 0.8568 (pt0) cc_final: 0.8114 (pm20) REVERT: B 298 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7726 (mm-30) REVERT: B 320 LYS cc_start: 0.8546 (tttt) cc_final: 0.8245 (ttpt) REVERT: C 140 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: C 196 ASN cc_start: 0.8468 (t0) cc_final: 0.8096 (m110) REVERT: C 198 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8270 (mt-10) REVERT: C 298 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7771 (mm-30) REVERT: D 140 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7811 (mm-30) REVERT: D 222 ASP cc_start: 0.8610 (t0) cc_final: 0.8200 (t70) REVERT: D 309 GLN cc_start: 0.7912 (mt0) cc_final: 0.7491 (pm20) REVERT: E 123 ARG cc_start: 0.7851 (mtp85) cc_final: 0.7510 (mtp85) REVERT: E 140 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: E 165 ASP cc_start: 0.8289 (m-30) cc_final: 0.7969 (t0) REVERT: E 288 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: E 315 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: E 320 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8298 (ttpt) REVERT: F 122 LYS cc_start: 0.7935 (mttt) cc_final: 0.7508 (mttp) REVERT: F 140 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7704 (mt-10) REVERT: F 189 ASP cc_start: 0.8562 (t70) cc_final: 0.8267 (t0) REVERT: F 288 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7678 (mt0) REVERT: F 298 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7540 (mm-30) outliers start: 23 outliers final: 10 residues processed: 219 average time/residue: 0.5811 time to fit residues: 135.5419 Evaluate side-chains 211 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 315 GLU Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 288 GLN Chi-restraints excluded: chain F residue 310 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 0.0170 chunk 85 optimal weight: 0.0970 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 246 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN C 255 GLN C 272 GLN D 156 ASN D 196 ASN D 246 GLN D 311 GLN E 303 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.120879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.091217 restraints weight = 11254.054| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.02 r_work: 0.2869 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10758 Z= 0.092 Angle : 0.417 6.166 14562 Z= 0.227 Chirality : 0.040 0.119 1524 Planarity : 0.003 0.028 1818 Dihedral : 6.428 27.524 1572 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.65 % Allowed : 14.47 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.25), residues: 1230 helix: 1.37 (0.22), residues: 540 sheet: -0.16 (0.36), residues: 174 loop : 0.81 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.007 0.001 TYR E 212 PHE 0.007 0.001 PHE B 271 TRP 0.043 0.001 TRP B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (10758) covalent geometry : angle 0.41714 / 0.23 (14562) hydrogen bonds : bond 0.03941 / 2.60 ( 456) hydrogen bonds : angle 4.66404 / 3.37 ( 1284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 0.348 Fit side-chains REVERT: A 147 ASP cc_start: 0.8447 (m-30) cc_final: 0.8220 (m-30) REVERT: A 230 GLU cc_start: 0.8236 (pt0) cc_final: 0.7607 (tp30) REVERT: A 257 LYS cc_start: 0.9014 (mttt) cc_final: 0.8798 (mttm) REVERT: A 298 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7437 (mm-30) REVERT: A 320 LYS cc_start: 0.8595 (tttt) cc_final: 0.8351 (ttpm) REVERT: B 136 GLU cc_start: 0.7748 (tt0) cc_final: 0.7446 (tt0) REVERT: B 198 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7887 (mm-30) REVERT: B 230 GLU cc_start: 0.8554 (pt0) cc_final: 0.8064 (pm20) REVERT: B 298 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7836 (mm-30) REVERT: B 320 LYS cc_start: 0.8543 (tttt) cc_final: 0.8213 (ttpt) REVERT: C 140 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: C 196 ASN cc_start: 0.8468 (t0) cc_final: 0.8161 (m110) REVERT: C 198 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8200 (mm-30) REVERT: C 298 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7760 (mm-30) REVERT: D 140 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7774 (mm-30) REVERT: D 222 ASP cc_start: 0.8619 (t0) cc_final: 0.8212 (t70) REVERT: D 272 GLN cc_start: 0.8012 (mt0) cc_final: 0.7668 (pt0) REVERT: D 309 GLN cc_start: 0.7912 (mt0) cc_final: 0.7517 (pm20) REVERT: E 123 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7560 (mtp85) REVERT: E 165 ASP cc_start: 0.8248 (m-30) cc_final: 0.7913 (t0) REVERT: E 288 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7736 (mt0) REVERT: E 315 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: E 320 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8288 (ttpt) REVERT: F 122 LYS cc_start: 0.7932 (mttt) cc_final: 0.7490 (mttp) REVERT: F 140 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7713 (mt-10) REVERT: F 189 ASP cc_start: 0.8559 (t70) cc_final: 0.8248 (t0) REVERT: F 204 GLU cc_start: 0.7511 (tt0) cc_final: 0.7131 (tp30) REVERT: F 273 TRP cc_start: 0.7039 (p-90) cc_final: 0.6614 (p-90) REVERT: F 281 ILE cc_start: 0.7981 (mp) cc_final: 0.7756 (pt) REVERT: F 288 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7684 (mt0) REVERT: F 298 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7607 (mm-30) outliers start: 18 outliers final: 4 residues processed: 220 average time/residue: 0.5318 time to fit residues: 124.6727 Evaluate side-chains 216 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 207 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 315 GLU Chi-restraints excluded: chain F residue 288 GLN Chi-restraints excluded: chain F residue 310 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN C 168 GLN C 246 GLN C 255 GLN C 272 GLN C 311 GLN D 156 ASN D 168 GLN D 196 ASN D 246 GLN D 311 GLN E 303 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.084985 restraints weight = 11190.687| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.04 r_work: 0.2771 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10758 Z= 0.272 Angle : 0.607 6.337 14562 Z= 0.318 Chirality : 0.047 0.166 1524 Planarity : 0.005 0.047 1818 Dihedral : 9.352 49.011 1572 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.29 % Allowed : 13.74 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.24), residues: 1230 helix: 0.96 (0.22), residues: 540 sheet: -0.23 (0.36), residues: 174 loop : 0.53 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 291 TYR 0.023 0.002 TYR E 212 PHE 0.013 0.002 PHE E 223 TRP 0.049 0.002 TRP B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.27 (10758) covalent geometry : angle 0.60730 / 0.32 (14562) hydrogen bonds : bond 0.06459 / 4.26 ( 456) hydrogen bonds : angle 4.97586 / 3.59 ( 1284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.8486 (m-30) cc_final: 0.8227 (m-30) REVERT: A 230 GLU cc_start: 0.8341 (pt0) cc_final: 0.7700 (tp30) REVERT: A 298 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7407 (mm-30) REVERT: A 320 LYS cc_start: 0.8603 (tttt) cc_final: 0.8354 (ttpm) REVERT: B 136 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: B 198 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7918 (mm-30) REVERT: B 230 GLU cc_start: 0.8600 (pt0) cc_final: 0.8105 (pm20) REVERT: B 298 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7676 (mm-30) REVERT: B 320 LYS cc_start: 0.8530 (tttt) cc_final: 0.8217 (ttpt) REVERT: C 196 ASN cc_start: 0.8476 (t0) cc_final: 0.8077 (m110) REVERT: C 198 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8264 (mt-10) REVERT: C 257 LYS cc_start: 0.9003 (mttt) cc_final: 0.8762 (mttp) REVERT: C 298 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7716 (mm-30) REVERT: D 140 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7834 (mm-30) REVERT: D 222 ASP cc_start: 0.8647 (t0) cc_final: 0.8235 (t70) REVERT: D 309 GLN cc_start: 0.7894 (mt0) cc_final: 0.7479 (pm20) REVERT: E 123 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7636 (mtp85) REVERT: E 165 ASP cc_start: 0.8319 (m-30) cc_final: 0.7966 (t0) REVERT: E 288 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: E 315 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: E 320 LYS cc_start: 0.8704 (ttpp) cc_final: 0.8363 (ttpt) REVERT: F 122 LYS cc_start: 0.7987 (mttt) cc_final: 0.7560 (mttp) REVERT: F 127 GLU cc_start: 0.8256 (tt0) cc_final: 0.7778 (tm-30) REVERT: F 140 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7730 (mt-10) REVERT: F 298 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7516 (mm-30) outliers start: 25 outliers final: 10 residues processed: 209 average time/residue: 0.5420 time to fit residues: 120.7938 Evaluate side-chains 205 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 315 GLU Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 310 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 116 optimal weight: 0.4980 chunk 95 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN D 196 ASN D 246 GLN D 311 GLN E 303 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.117994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.087896 restraints weight = 11258.244| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.02 r_work: 0.2817 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10758 Z= 0.137 Angle : 0.487 7.028 14562 Z= 0.263 Chirality : 0.042 0.133 1524 Planarity : 0.004 0.030 1818 Dihedral : 7.755 40.223 1572 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.28 % Allowed : 14.93 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1230 helix: 1.07 (0.22), residues: 540 sheet: -0.25 (0.36), residues: 174 loop : 0.64 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.013 0.001 TYR E 212 PHE 0.008 0.001 PHE E 271 TRP 0.036 0.001 TRP B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (10758) covalent geometry : angle 0.48703 / 0.26 (14562) hydrogen bonds : bond 0.04945 / 3.27 ( 456) hydrogen bonds : angle 4.80982 / 3.48 ( 1284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 147 ASP cc_start: 0.8487 (m-30) cc_final: 0.8223 (m-30) REVERT: A 230 GLU cc_start: 0.8283 (pt0) cc_final: 0.7622 (tp30) REVERT: A 298 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7413 (mm-30) REVERT: A 320 LYS cc_start: 0.8622 (tttt) cc_final: 0.8363 (ttpm) REVERT: B 136 GLU cc_start: 0.7767 (tt0) cc_final: 0.7462 (tt0) REVERT: B 198 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7906 (mm-30) REVERT: B 230 GLU cc_start: 0.8553 (pt0) cc_final: 0.8105 (pm20) REVERT: B 298 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7734 (mm-30) REVERT: B 320 LYS cc_start: 0.8536 (tttt) cc_final: 0.8234 (ttpt) REVERT: C 140 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: C 196 ASN cc_start: 0.8468 (t0) cc_final: 0.8095 (m110) REVERT: C 198 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8264 (mt-10) REVERT: C 298 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7679 (mm-30) REVERT: D 140 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7831 (mm-30) REVERT: D 222 ASP cc_start: 0.8614 (t0) cc_final: 0.8209 (t70) REVERT: D 309 GLN cc_start: 0.7898 (mt0) cc_final: 0.7508 (pm20) REVERT: E 123 ARG cc_start: 0.7899 (mtp85) cc_final: 0.7655 (mtp85) REVERT: E 140 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: E 165 ASP cc_start: 0.8291 (m-30) cc_final: 0.7969 (t0) REVERT: E 288 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7956 (mt0) REVERT: E 315 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: E 320 LYS cc_start: 0.8633 (ttpp) cc_final: 0.8299 (ttpt) REVERT: F 122 LYS cc_start: 0.7961 (mttt) cc_final: 0.7542 (mttp) REVERT: F 127 GLU cc_start: 0.8236 (tt0) cc_final: 0.7771 (tm-30) REVERT: F 140 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7752 (mt-10) REVERT: F 189 ASP cc_start: 0.8569 (t70) cc_final: 0.8262 (t0) REVERT: F 288 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7694 (mt0) REVERT: F 298 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7526 (mm-30) outliers start: 14 outliers final: 5 residues processed: 208 average time/residue: 0.5089 time to fit residues: 113.1501 Evaluate side-chains 207 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 315 GLU Chi-restraints excluded: chain F residue 288 GLN Chi-restraints excluded: chain F residue 310 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 38 optimal weight: 0.0270 chunk 65 optimal weight: 3.9990 chunk 4 optimal weight: 0.0870 chunk 103 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 161 GLN A 246 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN C 255 GLN C 272 GLN D 156 ASN D 196 ASN D 246 GLN D 311 GLN E 303 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.089248 restraints weight = 11345.493| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.07 r_work: 0.2828 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10758 Z= 0.094 Angle : 0.428 7.623 14562 Z= 0.234 Chirality : 0.040 0.120 1524 Planarity : 0.003 0.031 1818 Dihedral : 6.465 26.737 1572 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.37 % Allowed : 14.93 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.24), residues: 1230 helix: 1.30 (0.22), residues: 540 sheet: 0.84 (0.45), residues: 114 loop : 0.74 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 319 TYR 0.007 0.001 TYR E 212 PHE 0.006 0.001 PHE A 271 TRP 0.015 0.001 TRP A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (10758) covalent geometry : angle 0.42844 / 0.23 (14562) hydrogen bonds : bond 0.03988 / 2.63 ( 456) hydrogen bonds : angle 4.66485 / 3.37 ( 1284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.328 Fit side-chains REVERT: A 147 ASP cc_start: 0.8444 (m-30) cc_final: 0.8198 (m-30) REVERT: A 230 GLU cc_start: 0.8239 (pt0) cc_final: 0.7508 (tp30) REVERT: A 257 LYS cc_start: 0.8976 (mttt) cc_final: 0.8738 (mttm) REVERT: A 298 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7379 (mm-30) REVERT: A 320 LYS cc_start: 0.8548 (tttt) cc_final: 0.8312 (ttpm) REVERT: B 136 GLU cc_start: 0.7700 (tt0) cc_final: 0.7391 (tt0) REVERT: B 198 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7857 (mm-30) REVERT: B 230 GLU cc_start: 0.8544 (pt0) cc_final: 0.8070 (pm20) REVERT: B 298 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7825 (mm-30) REVERT: B 320 LYS cc_start: 0.8481 (tttt) cc_final: 0.8144 (ttpt) REVERT: C 196 ASN cc_start: 0.8446 (t0) cc_final: 0.8120 (m110) REVERT: C 198 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8106 (mm-30) REVERT: C 298 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7683 (mm-30) REVERT: D 140 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7707 (mm-30) REVERT: D 222 ASP cc_start: 0.8632 (t0) cc_final: 0.8206 (t70) REVERT: D 272 GLN cc_start: 0.7997 (mt0) cc_final: 0.7650 (pt0) REVERT: D 309 GLN cc_start: 0.7903 (mt0) cc_final: 0.7493 (pm20) REVERT: E 123 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7587 (mtp85) REVERT: E 124 GLU cc_start: 0.7031 (pp20) cc_final: 0.6779 (tp30) REVERT: E 140 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: E 165 ASP cc_start: 0.8197 (m-30) cc_final: 0.7844 (t0) REVERT: E 288 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7738 (mt0) REVERT: E 320 LYS cc_start: 0.8534 (ttpp) cc_final: 0.8221 (ttpt) REVERT: F 127 GLU cc_start: 0.8191 (tt0) cc_final: 0.7703 (tm-30) REVERT: F 140 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7720 (mt-10) REVERT: F 189 ASP cc_start: 0.8489 (t70) cc_final: 0.8203 (t0) REVERT: F 273 TRP cc_start: 0.7043 (p-90) cc_final: 0.6573 (p-90) REVERT: F 281 ILE cc_start: 0.7929 (mp) cc_final: 0.7667 (pt) REVERT: F 298 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7511 (mm-30) outliers start: 15 outliers final: 6 residues processed: 209 average time/residue: 0.5095 time to fit residues: 113.7675 Evaluate side-chains 206 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 197 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain F residue 310 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 11 optimal weight: 0.0050 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN C 255 GLN C 272 GLN C 311 GLN D 156 ASN D 196 ASN D 246 GLN D 311 GLN E 303 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.088962 restraints weight = 11377.887| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.08 r_work: 0.2826 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10758 Z= 0.099 Angle : 0.438 7.802 14562 Z= 0.238 Chirality : 0.040 0.120 1524 Planarity : 0.003 0.031 1818 Dihedral : 6.551 26.324 1572 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.37 % Allowed : 14.74 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.24), residues: 1230 helix: 1.35 (0.22), residues: 546 sheet: 0.91 (0.45), residues: 114 loop : 0.84 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 319 TYR 0.009 0.001 TYR A 295 PHE 0.007 0.001 PHE A 271 TRP 0.014 0.001 TRP A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (10758) covalent geometry : angle 0.43773 / 0.24 (14562) hydrogen bonds : bond 0.04089 / 2.70 ( 456) hydrogen bonds : angle 4.62996 / 3.35 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4081.98 seconds wall clock time: 69 minutes 56.92 seconds (4196.92 seconds total)