Starting phenix.real_space_refine on Wed Mar 4 04:30:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pqj_71784/03_2026/9pqj_71784.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pqj_71784/03_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_71784/03_2026/9pqj_71784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pqj_71784/03_2026/9pqj_71784.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pqj_71784/03_2026/9pqj_71784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pqj_71784/03_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-5986/lib/python3.9/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: 2.71, 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: 0.82 Conformation dependent library (CDL) restraints added in 491.0 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: 0.39 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: 1.54 Time building geometry restraints manager: 1.12 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=" CA THR B 184 " pdb=" C THR B 184 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.29e-02 6.01e+03 5.68e+00 bond pdb=" C THR F 184 " pdb=" O THR F 184 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.17e-02 7.31e+03 5.53e+00 bond pdb=" C THR C 184 " pdb=" O THR C 184 " ideal model delta sigma weight residual 1.237 1.210 0.026 1.19e-02 7.06e+03 4.90e+00 bond pdb=" C THR E 184 " pdb=" O THR E 184 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.17e-02 7.31e+03 4.56e+00 bond pdb=" CA THR C 184 " pdb=" C THR C 184 " ideal model delta sigma weight residual 1.524 1.496 0.027 1.29e-02 6.01e+03 4.40e+00 ... (remaining 10753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 13886 1.08 - 2.15: 528 2.15 - 3.23: 118 3.23 - 4.31: 26 4.31 - 5.39: 4 Bond angle restraints: 14562 Sorted by residual: angle pdb=" CA THR C 184 " pdb=" CB THR C 184 " pdb=" OG1 THR C 184 " ideal model delta sigma weight residual 109.60 105.12 4.48 1.50e+00 4.44e-01 8.92e+00 angle pdb=" C GLU A 204 " pdb=" CA GLU A 204 " pdb=" CB GLU A 204 " ideal model delta sigma weight residual 110.42 115.81 -5.39 1.99e+00 2.53e-01 7.33e+00 angle pdb=" CA THR F 184 " pdb=" C THR F 184 " pdb=" O THR F 184 " ideal model delta sigma weight residual 120.55 117.88 2.67 1.06e+00 8.90e-01 6.33e+00 angle pdb=" CA THR A 184 " pdb=" CB THR A 184 " pdb=" OG1 THR A 184 " ideal model delta sigma weight residual 109.60 105.86 3.74 1.50e+00 4.44e-01 6.20e+00 angle pdb=" CA THR B 184 " pdb=" C THR B 184 " pdb=" O THR B 184 " ideal model delta sigma weight residual 120.42 117.84 2.58 1.06e+00 8.90e-01 5.92e+00 ... (remaining 14557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 5655 15.67 - 31.34: 522 31.34 - 47.01: 129 47.01 - 62.68: 82 62.68 - 78.35: 32 Dihedral angle restraints: 6420 sinusoidal: 2826 harmonic: 3594 Sorted by residual: 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=" CA GLN F 246 " pdb=" C GLN F 246 " pdb=" N VAL F 247 " pdb=" CA VAL F 247 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA GLN C 246 " pdb=" C GLN C 246 " pdb=" N VAL C 247 " pdb=" CA VAL C 247 " ideal model delta harmonic sigma weight residual 180.00 163.91 16.09 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 6417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1037 0.037 - 0.075: 341 0.075 - 0.112: 143 0.112 - 0.149: 11 0.149 - 0.187: 4 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CA THR F 184 " pdb=" N THR F 184 " pdb=" C THR F 184 " pdb=" CB THR F 184 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CB THR B 184 " pdb=" CA THR B 184 " pdb=" OG1 THR B 184 " pdb=" CG2 THR B 184 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CB THR D 184 " pdb=" CA THR D 184 " pdb=" OG1 THR D 184 " pdb=" CG2 THR D 184 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 1533 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.060 Find NCS groups from input model: 0.260 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:7.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 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 : 0.004 0.031 10758 Z= 0.182 Angle : 0.521 5.386 14562 Z= 0.294 Chirality : 0.043 0.187 1536 Planarity : 0.004 0.039 1818 Dihedral : 15.373 78.354 4104 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 covalent geometry : bond 0.00385 (10758) covalent geometry : angle 0.52115 (14562) hydrogen bonds : bond 0.14113 ( 456) hydrogen bonds : angle 6.36445 ( 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 : 0.446 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: 0.7893 time to fit residues: 244.0503 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 : 0.334 ------------------------------------------------------------------------------- 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: 3.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 4.9990 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: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 156 ASN D 246 GLN D 288 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.116311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.086103 restraints weight = 11417.623| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.03 r_work: 0.2772 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10758 Z= 0.230 Angle : 0.579 7.179 14562 Z= 0.309 Chirality : 0.045 0.136 1536 Planarity : 0.005 0.045 1818 Dihedral : 13.286 81.587 1464 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.74 % Allowed : 8.97 % 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: 0.82 (0.24), residues: 1230 helix: 0.98 (0.22), residues: 540 sheet: 0.03 (0.37), residues: 174 loop : 0.47 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 224 TYR 0.020 0.002 TYR A 212 PHE 0.011 0.002 PHE E 223 TRP 0.024 0.002 TRP A 273 Details of bonding type rmsd covalent geometry : bond 0.00544 (10758) covalent geometry : angle 0.57882 (14562) hydrogen bonds : bond 0.06345 ( 456) hydrogen bonds : angle 5.20188 ( 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 231 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 212 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 198 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8054 (tt0) REVERT: A 230 GLU cc_start: 0.8261 (pt0) cc_final: 0.7541 (tp30) REVERT: A 295 TYR cc_start: 0.8452 (t80) cc_final: 0.8250 (t80) REVERT: A 298 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7433 (mm-30) REVERT: A 320 LYS cc_start: 0.8621 (tttt) cc_final: 0.8296 (ttpm) REVERT: B 198 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7922 (mm-30) REVERT: B 230 GLU cc_start: 0.8544 (pt0) cc_final: 0.8110 (pm20) REVERT: B 298 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7844 (mm-30) REVERT: B 320 LYS cc_start: 0.8548 (tttt) cc_final: 0.8241 (ttpt) REVERT: C 140 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7700 (mp0) REVERT: C 196 ASN cc_start: 0.8553 (t0) cc_final: 0.8139 (m110) REVERT: C 198 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8258 (mt-10) REVERT: C 298 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7757 (mm-30) REVERT: D 140 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7817 (mm-30) REVERT: D 230 GLU cc_start: 0.8283 (pt0) cc_final: 0.8053 (tp30) REVERT: D 309 GLN cc_start: 0.7908 (mt0) cc_final: 0.7444 (pm20) REVERT: E 123 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7524 (mtp85) REVERT: E 165 ASP cc_start: 0.8338 (m-30) cc_final: 0.7980 (t0) REVERT: E 288 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7966 (mt0) REVERT: E 315 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: F 122 LYS cc_start: 0.7887 (mttt) cc_final: 0.7544 (mttp) REVERT: F 127 GLU cc_start: 0.8244 (tt0) cc_final: 0.7752 (tm-30) REVERT: F 135 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7130 (tmt170) REVERT: F 178 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8502 (mm-30) REVERT: F 298 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7549 (mm-30) outliers start: 19 outliers final: 6 residues processed: 219 average time/residue: 0.7069 time to fit residues: 163.9267 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 : 0.409 ------------------------------------------------------------------------------- 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 198 GLU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 308 ASN 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 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: 0.5980 chunk 78 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.088829 restraints weight = 11368.414| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.03 r_work: 0.2823 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 10758 Z= 0.108 Angle : 0.457 5.839 14562 Z= 0.248 Chirality : 0.041 0.120 1536 Planarity : 0.003 0.031 1818 Dihedral : 13.087 88.257 1464 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.83 % Allowed : 10.90 % Favored : 87.27 % 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: 1.02 (0.24), residues: 1230 helix: 1.17 (0.22), residues: 540 sheet: -0.07 (0.36), residues: 174 loop : 0.63 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 319 TYR 0.009 0.001 TYR A 212 PHE 0.006 0.001 PHE F 271 TRP 0.021 0.001 TRP B 273 Details of bonding type rmsd covalent geometry : bond 0.00230 (10758) covalent geometry : angle 0.45677 (14562) hydrogen bonds : bond 0.04664 ( 456) hydrogen bonds : angle 4.91206 ( 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 227 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 230 GLU cc_start: 0.8242 (pt0) cc_final: 0.7517 (tp30) REVERT: A 298 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7424 (mm-30) REVERT: A 319 ARG cc_start: 0.8449 (mtt-85) cc_final: 0.8136 (mtt-85) REVERT: A 320 LYS cc_start: 0.8623 (tttt) cc_final: 0.8298 (ttpm) REVERT: B 136 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7292 (tt0) REVERT: B 198 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7854 (mm-30) REVERT: B 230 GLU cc_start: 0.8537 (pt0) cc_final: 0.8105 (pm20) REVERT: B 298 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7813 (mm-30) REVERT: B 320 LYS cc_start: 0.8563 (tttt) cc_final: 0.8238 (ttpt) REVERT: C 139 MET cc_start: 0.8713 (mmt) cc_final: 0.8487 (mmm) REVERT: C 140 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7699 (mp0) REVERT: C 196 ASN cc_start: 0.8538 (t0) cc_final: 0.8178 (m110) REVERT: C 198 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8163 (mm-30) REVERT: C 298 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7746 (mm-30) REVERT: D 140 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7808 (mm-30) REVERT: D 309 GLN cc_start: 0.7884 (mt0) cc_final: 0.7450 (pm20) REVERT: E 123 ARG cc_start: 0.7802 (mtp85) cc_final: 0.7451 (mtt180) REVERT: E 165 ASP cc_start: 0.8294 (m-30) cc_final: 0.7964 (t0) REVERT: E 288 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7880 (mt0) REVERT: E 315 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: F 122 LYS cc_start: 0.7911 (mttt) cc_final: 0.7517 (mttp) REVERT: F 127 GLU cc_start: 0.8230 (tt0) cc_final: 0.7752 (tm-30) REVERT: F 135 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7184 (tmt170) REVERT: F 178 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8486 (mm-30) REVERT: F 298 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7653 (mm-30) outliers start: 20 outliers final: 4 residues processed: 215 average time/residue: 0.6837 time to fit residues: 155.9528 Evaluate side-chains 208 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 198 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ASN 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 308 ASN 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 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: 0.9990 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 87 optimal weight: 0.8980 chunk 93 optimal weight: 0.0770 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 246 GLN B 246 GLN C 161 GLN C 246 GLN C 255 GLN C 272 GLN C 311 GLN 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 = 0.3427 r_free = 0.3427 target = 0.119700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.089682 restraints weight = 11388.151| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.02 r_work: 0.2838 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10758 Z= 0.098 Angle : 0.438 5.632 14562 Z= 0.236 Chirality : 0.040 0.121 1536 Planarity : 0.003 0.028 1818 Dihedral : 12.917 89.971 1464 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.11 % Allowed : 11.81 % Favored : 86.08 % 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: 1.13 (0.24), residues: 1230 helix: 1.29 (0.22), residues: 540 sheet: -0.14 (0.36), residues: 174 loop : 0.72 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 224 TYR 0.008 0.001 TYR E 212 PHE 0.006 0.001 PHE F 271 TRP 0.024 0.001 TRP B 273 Details of bonding type rmsd covalent geometry : bond 0.00208 (10758) covalent geometry : angle 0.43783 (14562) hydrogen bonds : bond 0.04319 ( 456) hydrogen bonds : angle 4.80196 ( 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 232 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.8262 (pt0) cc_final: 0.7523 (tp30) REVERT: A 281 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7568 (pp) REVERT: A 298 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7452 (mm-30) REVERT: A 319 ARG cc_start: 0.8431 (mtt-85) cc_final: 0.8110 (mtt-85) REVERT: A 320 LYS cc_start: 0.8609 (tttt) cc_final: 0.8332 (ttpm) REVERT: B 136 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7297 (tt0) REVERT: B 230 GLU cc_start: 0.8513 (pt0) cc_final: 0.8082 (pm20) REVERT: B 298 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7831 (mm-30) REVERT: B 320 LYS cc_start: 0.8530 (tttt) cc_final: 0.8205 (ttpt) REVERT: C 196 ASN cc_start: 0.8483 (t0) cc_final: 0.8123 (m110) REVERT: C 198 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8132 (mm-30) REVERT: C 298 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7784 (mm-30) REVERT: D 140 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7807 (mm-30) REVERT: D 272 GLN cc_start: 0.8028 (mt0) cc_final: 0.7659 (pt0) REVERT: D 309 GLN cc_start: 0.7876 (mt0) cc_final: 0.7441 (pm20) REVERT: E 123 ARG cc_start: 0.7797 (mtp85) cc_final: 0.7437 (mtt180) REVERT: E 140 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: E 165 ASP cc_start: 0.8272 (m-30) cc_final: 0.7963 (t0) REVERT: E 288 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7804 (mt0) REVERT: E 315 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: F 122 LYS cc_start: 0.7912 (mttt) cc_final: 0.7508 (mttp) REVERT: F 127 GLU cc_start: 0.8245 (tt0) cc_final: 0.7762 (tm-30) REVERT: F 135 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7102 (tmt170) REVERT: F 139 MET cc_start: 0.8736 (mmp) cc_final: 0.8420 (mmm) REVERT: F 178 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8449 (mm-30) REVERT: F 189 ASP cc_start: 0.8609 (t70) cc_final: 0.8291 (t0) REVERT: F 298 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7666 (mm-30) outliers start: 23 outliers final: 7 residues processed: 218 average time/residue: 0.6996 time to fit residues: 161.7755 Evaluate side-chains 218 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 281 ILE 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 308 ASN Chi-restraints excluded: chain D residue 127 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 135 ARG Chi-restraints excluded: chain F residue 178 GLU 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: 0.9990 chunk 20 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 0.0980 chunk 80 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 246 GLN B 246 GLN C 161 GLN C 255 GLN C 272 GLN C 311 GLN D 131 ASN D 156 ASN 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 = 0.3400 r_free = 0.3400 target = 0.117713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.087551 restraints weight = 11359.772| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.02 r_work: 0.2802 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10758 Z= 0.147 Angle : 0.485 6.193 14562 Z= 0.259 Chirality : 0.042 0.130 1536 Planarity : 0.003 0.030 1818 Dihedral : 13.086 87.016 1464 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.29 % Allowed : 12.91 % Favored : 84.80 % 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: 1.03 (0.24), residues: 1230 helix: 1.19 (0.22), residues: 540 sheet: -0.15 (0.36), residues: 174 loop : 0.65 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 135 TYR 0.015 0.002 TYR E 212 PHE 0.009 0.001 PHE A 271 TRP 0.028 0.001 TRP B 273 Details of bonding type rmsd covalent geometry : bond 0.00338 (10758) covalent geometry : angle 0.48534 (14562) hydrogen bonds : bond 0.05078 ( 456) hydrogen bonds : angle 4.83726 ( 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 228 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.7696 (tt0) cc_final: 0.7333 (tt0) REVERT: A 230 GLU cc_start: 0.8216 (pt0) cc_final: 0.7562 (tp30) REVERT: A 298 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7419 (mm-30) REVERT: A 319 ARG cc_start: 0.8449 (mtt-85) cc_final: 0.8132 (mtt-85) REVERT: A 320 LYS cc_start: 0.8611 (tttt) cc_final: 0.8339 (ttpm) REVERT: B 136 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7372 (tt0) REVERT: B 198 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7838 (mm-30) REVERT: B 230 GLU cc_start: 0.8523 (pt0) cc_final: 0.8055 (pm20) REVERT: B 298 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7848 (mm-30) REVERT: B 320 LYS cc_start: 0.8539 (tttt) cc_final: 0.8211 (ttpt) REVERT: C 140 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: C 196 ASN cc_start: 0.8504 (t0) cc_final: 0.8152 (m110) REVERT: C 198 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8137 (mm-30) REVERT: C 298 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7765 (mm-30) REVERT: D 140 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7819 (mm-30) REVERT: D 272 GLN cc_start: 0.8054 (mt0) cc_final: 0.7648 (pt0) REVERT: D 309 GLN cc_start: 0.7872 (mt0) cc_final: 0.7467 (pm20) REVERT: E 123 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7503 (mtp85) REVERT: E 140 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: E 165 ASP cc_start: 0.8281 (m-30) cc_final: 0.7973 (t0) REVERT: E 288 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7930 (mt0) REVERT: E 315 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: E 320 LYS cc_start: 0.8678 (ttpp) cc_final: 0.8351 (ttpt) REVERT: F 122 LYS cc_start: 0.7957 (mttt) cc_final: 0.7548 (mttp) REVERT: F 127 GLU cc_start: 0.8251 (tt0) cc_final: 0.7769 (tm-30) REVERT: F 139 MET cc_start: 0.8772 (mmp) cc_final: 0.8559 (mmm) REVERT: F 204 GLU cc_start: 0.7440 (tt0) cc_final: 0.7008 (tp30) REVERT: F 298 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7643 (mm-30) outliers start: 25 outliers final: 8 residues processed: 215 average time/residue: 0.6998 time to fit residues: 159.9529 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 : 0.430 ------------------------------------------------------------------------------- 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 D residue 127 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 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: 1.9990 chunk 67 optimal weight: 4.9990 chunk 115 optimal weight: 0.0270 chunk 63 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 246 GLN B 246 GLN C 246 GLN C 311 GLN D 131 ASN 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 = 0.3415 r_free = 0.3415 target = 0.118851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.088809 restraints weight = 11445.811| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.02 r_work: 0.2822 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10758 Z= 0.112 Angle : 0.450 5.874 14562 Z= 0.242 Chirality : 0.041 0.122 1536 Planarity : 0.003 0.028 1818 Dihedral : 12.927 88.863 1464 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.11 % Allowed : 13.28 % Favored : 84.62 % 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: 1.13 (0.24), residues: 1230 helix: 1.29 (0.22), residues: 540 sheet: -0.16 (0.36), residues: 174 loop : 0.71 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 319 TYR 0.010 0.001 TYR E 212 PHE 0.007 0.001 PHE A 271 TRP 0.033 0.001 TRP B 273 Details of bonding type rmsd covalent geometry : bond 0.00246 (10758) covalent geometry : angle 0.45010 (14562) hydrogen bonds : bond 0.04513 ( 456) hydrogen bonds : angle 4.77418 ( 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 226 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 230 GLU cc_start: 0.8193 (pt0) cc_final: 0.7554 (tp30) REVERT: A 298 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7403 (mm-30) REVERT: A 319 ARG cc_start: 0.8428 (mtt-85) cc_final: 0.8195 (mtt-85) REVERT: A 320 LYS cc_start: 0.8601 (tttt) cc_final: 0.8328 (ttpm) REVERT: B 136 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: B 230 GLU cc_start: 0.8531 (pt0) cc_final: 0.8085 (pm20) REVERT: B 298 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7858 (mm-30) REVERT: B 320 LYS cc_start: 0.8542 (tttt) cc_final: 0.8199 (ttpt) REVERT: C 196 ASN cc_start: 0.8481 (t0) cc_final: 0.8125 (m110) REVERT: C 198 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8135 (mm-30) REVERT: C 298 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7759 (mm-30) REVERT: D 140 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7767 (mm-30) REVERT: D 222 ASP cc_start: 0.8650 (t0) cc_final: 0.8243 (t70) REVERT: D 272 GLN cc_start: 0.8035 (mt0) cc_final: 0.7646 (pt0) REVERT: D 309 GLN cc_start: 0.7875 (mt0) cc_final: 0.7450 (pm20) REVERT: E 123 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7373 (mtt-85) REVERT: E 140 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: E 165 ASP cc_start: 0.8270 (m-30) cc_final: 0.7970 (t0) REVERT: E 288 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7852 (mt0) REVERT: E 315 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: E 320 LYS cc_start: 0.8692 (ttpp) cc_final: 0.8360 (ttpt) REVERT: F 122 LYS cc_start: 0.7941 (mttt) cc_final: 0.7524 (mttp) REVERT: F 135 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7001 (tmt170) REVERT: F 139 MET cc_start: 0.8735 (mmp) cc_final: 0.8465 (mmm) REVERT: F 189 ASP cc_start: 0.8601 (t70) cc_final: 0.8298 (t0) REVERT: F 204 GLU cc_start: 0.7435 (tt0) cc_final: 0.6976 (tp30) REVERT: F 288 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: F 298 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7651 (mm-30) outliers start: 23 outliers final: 8 residues processed: 217 average time/residue: 0.6779 time to fit residues: 156.1470 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 : 0.397 ------------------------------------------------------------------------------- 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 268 SER Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 127 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 135 ARG 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: 2.9990 chunk 58 optimal weight: 0.9990 chunk 85 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.119103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.088831 restraints weight = 11235.929| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.04 r_work: 0.2828 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10758 Z= 0.109 Angle : 0.451 6.523 14562 Z= 0.242 Chirality : 0.041 0.122 1536 Planarity : 0.003 0.027 1818 Dihedral : 12.867 89.217 1464 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.20 % Allowed : 13.83 % 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: 1.16 (0.24), residues: 1230 helix: 1.32 (0.22), residues: 540 sheet: -0.15 (0.36), residues: 174 loop : 0.73 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 224 TYR 0.010 0.001 TYR E 212 PHE 0.008 0.001 PHE A 271 TRP 0.043 0.001 TRP B 273 Details of bonding type rmsd covalent geometry : bond 0.00236 (10758) covalent geometry : angle 0.45052 (14562) hydrogen bonds : bond 0.04443 ( 456) hydrogen bonds : angle 4.75025 ( 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 226 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.7743 (tt0) cc_final: 0.7368 (tt0) REVERT: A 230 GLU cc_start: 0.8203 (pt0) cc_final: 0.7563 (tp30) REVERT: A 298 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7381 (mm-30) REVERT: A 319 ARG cc_start: 0.8487 (mtt-85) cc_final: 0.8261 (mtt-85) REVERT: A 320 LYS cc_start: 0.8632 (tttt) cc_final: 0.8378 (ttpm) REVERT: B 136 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7368 (tt0) REVERT: B 198 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7868 (mm-30) REVERT: B 230 GLU cc_start: 0.8547 (pt0) cc_final: 0.8098 (pm20) REVERT: B 298 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7841 (mm-30) REVERT: B 320 LYS cc_start: 0.8565 (tttt) cc_final: 0.8248 (ttpt) REVERT: C 196 ASN cc_start: 0.8501 (t0) cc_final: 0.8171 (m110) REVERT: C 198 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8150 (mm-30) REVERT: C 298 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7757 (mm-30) REVERT: D 140 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7760 (mm-30) REVERT: D 222 ASP cc_start: 0.8634 (t0) cc_final: 0.8220 (t70) REVERT: D 272 GLN cc_start: 0.8041 (mt0) cc_final: 0.7685 (pt0) REVERT: D 298 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7730 (mt-10) REVERT: D 309 GLN cc_start: 0.7893 (mt0) cc_final: 0.7474 (pm20) REVERT: E 123 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7380 (mtt-85) REVERT: E 165 ASP cc_start: 0.8272 (m-30) cc_final: 0.7955 (t0) REVERT: E 288 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: E 315 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: E 320 LYS cc_start: 0.8713 (ttpp) cc_final: 0.8393 (ttpt) REVERT: F 122 LYS cc_start: 0.7940 (mttt) cc_final: 0.7527 (mttp) REVERT: F 135 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7002 (tmt170) REVERT: F 139 MET cc_start: 0.8724 (mmp) cc_final: 0.8442 (mmm) REVERT: F 189 ASP cc_start: 0.8559 (t70) cc_final: 0.8257 (t0) REVERT: F 204 GLU cc_start: 0.7454 (tt0) cc_final: 0.7083 (tp30) REVERT: F 288 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: F 298 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7628 (mm-30) outliers start: 24 outliers final: 10 residues processed: 216 average time/residue: 0.6655 time to fit residues: 152.5987 Evaluate side-chains 219 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 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 308 ASN Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 127 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 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: 1.9990 chunk 56 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 246 GLN B 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 = 0.3390 r_free = 0.3390 target = 0.116867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.086750 restraints weight = 11342.385| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.03 r_work: 0.2791 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10758 Z= 0.170 Angle : 0.520 7.145 14562 Z= 0.277 Chirality : 0.043 0.133 1536 Planarity : 0.004 0.031 1818 Dihedral : 13.173 85.200 1464 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.29 % Allowed : 13.83 % 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: 1.17 (0.24), residues: 1230 helix: 1.13 (0.22), residues: 540 sheet: 0.91 (0.46), residues: 114 loop : 0.57 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 319 TYR 0.017 0.002 TYR E 212 PHE 0.011 0.001 PHE E 223 TRP 0.051 0.002 TRP B 273 Details of bonding type rmsd covalent geometry : bond 0.00396 (10758) covalent geometry : angle 0.52014 (14562) hydrogen bonds : bond 0.05470 ( 456) hydrogen bonds : angle 4.86289 ( 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 219 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.7744 (tt0) cc_final: 0.7418 (tt0) REVERT: A 230 GLU cc_start: 0.8234 (pt0) cc_final: 0.7592 (tp30) REVERT: A 298 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7406 (mm-30) REVERT: A 320 LYS cc_start: 0.8624 (tttt) cc_final: 0.8372 (ttpm) REVERT: B 136 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: B 198 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7872 (mm-30) REVERT: B 230 GLU cc_start: 0.8552 (pt0) cc_final: 0.8083 (pm20) REVERT: B 298 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7791 (mm-30) REVERT: B 320 LYS cc_start: 0.8565 (tttt) cc_final: 0.8237 (ttpt) REVERT: C 196 ASN cc_start: 0.8470 (t0) cc_final: 0.8097 (m110) REVERT: C 198 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8233 (mt-10) REVERT: C 298 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7749 (mm-30) REVERT: D 140 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7854 (mm-30) REVERT: D 222 ASP cc_start: 0.8608 (t0) cc_final: 0.8189 (t70) REVERT: D 309 GLN cc_start: 0.7919 (mt0) cc_final: 0.7508 (pm20) REVERT: E 123 ARG cc_start: 0.7838 (mtp85) cc_final: 0.7494 (mtp85) REVERT: E 165 ASP cc_start: 0.8299 (m-30) cc_final: 0.7965 (t0) REVERT: E 288 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.7967 (mt0) REVERT: E 315 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: E 320 LYS cc_start: 0.8687 (ttpp) cc_final: 0.8363 (ttpt) REVERT: F 122 LYS cc_start: 0.7956 (mttt) cc_final: 0.7547 (mttp) REVERT: F 135 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.6983 (tmt170) REVERT: F 204 GLU cc_start: 0.7535 (tt0) cc_final: 0.7032 (tp30) REVERT: F 288 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7702 (mt0) REVERT: F 298 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7610 (mm-30) outliers start: 25 outliers final: 13 residues processed: 207 average time/residue: 0.6686 time to fit residues: 147.5512 Evaluate side-chains 213 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 B residue 281 ILE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 327 MET 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 288 GLN 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: 0.9980 chunk 20 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 246 GLN D 156 ASN D 196 ASN D 246 GLN D 311 GLN E 303 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.088413 restraints weight = 11282.949| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.02 r_work: 0.2825 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10758 Z= 0.113 Angle : 0.464 7.469 14562 Z= 0.250 Chirality : 0.041 0.122 1536 Planarity : 0.003 0.029 1818 Dihedral : 12.970 88.873 1464 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.01 % Allowed : 14.19 % 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: 1.09 (0.24), residues: 1230 helix: 1.24 (0.22), residues: 540 sheet: -0.20 (0.36), residues: 174 loop : 0.72 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 319 TYR 0.010 0.001 TYR E 212 PHE 0.008 0.001 PHE A 271 TRP 0.053 0.001 TRP B 273 Details of bonding type rmsd covalent geometry : bond 0.00247 (10758) covalent geometry : angle 0.46417 (14562) hydrogen bonds : bond 0.04556 ( 456) hydrogen bonds : angle 4.77676 ( 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 219 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.7706 (tt0) cc_final: 0.7331 (tt0) REVERT: A 230 GLU cc_start: 0.8242 (pt0) cc_final: 0.7594 (tp30) REVERT: A 298 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7399 (mm-30) REVERT: A 320 LYS cc_start: 0.8631 (tttt) cc_final: 0.8382 (ttpm) REVERT: B 136 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: B 198 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7879 (mm-30) REVERT: B 230 GLU cc_start: 0.8549 (pt0) cc_final: 0.8093 (pm20) REVERT: B 298 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7830 (mm-30) REVERT: B 320 LYS cc_start: 0.8564 (tttt) cc_final: 0.8240 (ttpt) REVERT: C 196 ASN cc_start: 0.8448 (t0) cc_final: 0.8115 (m110) REVERT: C 198 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8158 (mm-30) REVERT: C 298 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7756 (mm-30) REVERT: D 140 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7800 (mm-30) REVERT: D 222 ASP cc_start: 0.8639 (t0) cc_final: 0.8225 (t70) REVERT: D 272 GLN cc_start: 0.8057 (mt0) cc_final: 0.7674 (pt0) REVERT: D 309 GLN cc_start: 0.7926 (mt0) cc_final: 0.7499 (pm20) REVERT: E 123 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7476 (mtp85) REVERT: E 165 ASP cc_start: 0.8279 (m-30) cc_final: 0.7964 (t0) REVERT: E 288 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7882 (mt0) REVERT: E 315 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: E 320 LYS cc_start: 0.8689 (ttpp) cc_final: 0.8348 (ttpm) REVERT: F 122 LYS cc_start: 0.7946 (mttt) cc_final: 0.7533 (mttp) REVERT: F 135 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.6999 (tmt170) REVERT: F 189 ASP cc_start: 0.8599 (t70) cc_final: 0.8292 (t0) REVERT: F 204 GLU cc_start: 0.7543 (tt0) cc_final: 0.7176 (tp30) REVERT: F 288 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: F 298 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7624 (mm-30) outliers start: 22 outliers final: 10 residues processed: 210 average time/residue: 0.6417 time to fit residues: 143.6214 Evaluate side-chains 212 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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 281 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 327 MET 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 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: 0.0470 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.0020 chunk 37 optimal weight: 0.9980 overall best weight: 0.7488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 246 GLN B 246 GLN D 156 ASN D 196 ASN D 246 GLN D 311 GLN E 303 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.119342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.089234 restraints weight = 11259.863| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.02 r_work: 0.2839 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2179 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= 0.105 Angle : 0.458 7.801 14562 Z= 0.246 Chirality : 0.040 0.122 1536 Planarity : 0.003 0.029 1818 Dihedral : 12.827 89.816 1464 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.01 % Allowed : 14.56 % Favored : 83.42 % 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: 1.17 (0.24), residues: 1230 helix: 1.32 (0.22), residues: 540 sheet: -0.18 (0.36), residues: 174 loop : 0.76 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.009 0.001 TYR E 212 PHE 0.007 0.001 PHE A 271 TRP 0.059 0.001 TRP B 273 Details of bonding type rmsd covalent geometry : bond 0.00227 (10758) covalent geometry : angle 0.45770 (14562) hydrogen bonds : bond 0.04327 ( 456) hydrogen bonds : angle 4.73397 ( 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 222 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 204 GLU cc_start: 0.7720 (tt0) cc_final: 0.7403 (tt0) REVERT: A 230 GLU cc_start: 0.8252 (pt0) cc_final: 0.7612 (tp30) REVERT: A 295 TYR cc_start: 0.8399 (t80) cc_final: 0.8197 (t80) REVERT: A 298 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7417 (mm-30) REVERT: A 320 LYS cc_start: 0.8636 (tttt) cc_final: 0.8366 (ttpm) REVERT: B 136 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: B 198 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7871 (mm-30) REVERT: B 230 GLU cc_start: 0.8541 (pt0) cc_final: 0.8087 (pm20) REVERT: B 298 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7824 (mm-30) REVERT: B 320 LYS cc_start: 0.8565 (tttt) cc_final: 0.8251 (ttpt) REVERT: C 196 ASN cc_start: 0.8488 (t0) cc_final: 0.8169 (m110) REVERT: C 198 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8152 (mm-30) REVERT: C 298 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7719 (mm-30) REVERT: D 140 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7778 (mm-30) REVERT: D 222 ASP cc_start: 0.8635 (t0) cc_final: 0.8226 (t70) REVERT: D 272 GLN cc_start: 0.8044 (mt0) cc_final: 0.7703 (pt0) REVERT: D 298 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7692 (mt-10) REVERT: D 309 GLN cc_start: 0.7926 (mt0) cc_final: 0.7509 (pm20) REVERT: E 123 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7364 (mtt-85) REVERT: E 140 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: E 165 ASP cc_start: 0.8258 (m-30) cc_final: 0.7956 (t0) REVERT: E 288 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7812 (mt0) REVERT: E 315 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: E 320 LYS cc_start: 0.8691 (ttpp) cc_final: 0.8355 (ttpm) REVERT: F 122 LYS cc_start: 0.7938 (mttt) cc_final: 0.7523 (mttp) REVERT: F 135 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7013 (tmt170) REVERT: F 189 ASP cc_start: 0.8585 (t70) cc_final: 0.8290 (t0) REVERT: F 204 GLU cc_start: 0.7536 (tt0) cc_final: 0.7048 (tp30) REVERT: F 288 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7604 (mt0) REVERT: F 298 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7603 (mm-30) outliers start: 22 outliers final: 7 residues processed: 212 average time/residue: 0.6507 time to fit residues: 146.8531 Evaluate side-chains 211 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 chunk 90 optimal weight: 5.9990 chunk 102 optimal weight: 0.0470 chunk 1 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 246 GLN 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 = 0.3423 r_free = 0.3423 target = 0.119198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.089075 restraints weight = 11273.282| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.02 r_work: 0.2835 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2195 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= 0.111 Angle : 0.463 7.813 14562 Z= 0.249 Chirality : 0.041 0.123 1536 Planarity : 0.003 0.029 1818 Dihedral : 12.794 89.377 1464 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.83 % Allowed : 14.56 % Favored : 83.61 % 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: 1.39 (0.24), residues: 1230 helix: 1.32 (0.22), residues: 540 sheet: 0.95 (0.46), residues: 114 loop : 0.71 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 319 TYR 0.010 0.001 TYR E 212 PHE 0.008 0.001 PHE A 271 TRP 0.035 0.001 TRP B 273 Details of bonding type rmsd covalent geometry : bond 0.00244 (10758) covalent geometry : angle 0.46327 (14562) hydrogen bonds : bond 0.04393 ( 456) hydrogen bonds : angle 4.72988 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4823.84 seconds wall clock time: 82 minutes 27.27 seconds (4947.27 seconds total)