Starting phenix.real_space_refine on Fri Aug 22 19:30:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlo_36402/08_2025/8jlo_36402.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlo_36402/08_2025/8jlo_36402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jlo_36402/08_2025/8jlo_36402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlo_36402/08_2025/8jlo_36402.map" model { file = "/net/cci-nas-00/data/ceres_data/8jlo_36402/08_2025/8jlo_36402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlo_36402/08_2025/8jlo_36402.cif" } resolution = 3.52 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= -0.001 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 4690 2.51 5 N 1266 2.21 5 O 1328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7343 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1972 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2321 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 11, 'TRANS': 274} Chain breaks: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UJL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.49, per 1000 atoms: 0.20 Number of scatterers: 7343 At special positions: 0 Unit cell: (74.8, 102.85, 131.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1328 8.00 N 1266 7.00 C 4690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 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: 0.48 Conformation dependent library (CDL) restraints added in 469.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 46.3% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 13 through 38 removed outlier: 3.505A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.794A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.184A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.772A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.879A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.564A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.658A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'R' and resid 22 through 51 removed outlier: 3.647A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 76 removed outlier: 3.592A pdb=" N TRP R 60 " --> pdb=" O THR R 56 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL R 76 " --> pdb=" O LEU R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 87 Processing helix chain 'R' and resid 92 through 125 removed outlier: 3.808A pdb=" N SER R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 161 removed outlier: 3.715A pdb=" N VAL R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 169 through 176 Processing helix chain 'R' and resid 187 through 199 removed outlier: 4.024A pdb=" N VAL R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 233 removed outlier: 3.888A pdb=" N ILE R 233 " --> pdb=" O GLN R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 277 removed outlier: 3.953A pdb=" N ILE R 255 " --> pdb=" O LYS R 251 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL R 256 " --> pdb=" O THR R 252 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 282 through 299 removed outlier: 3.818A pdb=" N ASN R 286 " --> pdb=" O PRO R 282 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL R 288 " --> pdb=" O THR R 284 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 319 removed outlier: 3.690A pdb=" N ARG R 312 " --> pdb=" O TYR R 308 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 24 Processing helix chain 'Y' and resid 29 through 44 removed outlier: 3.564A pdb=" N ALA Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS Y 44 " --> pdb=" O TYR Y 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214 removed outlier: 10.223A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.764A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.988A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.647A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.491A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.585A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.958A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 361 hydrogen bonds defined for protein. 1050 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: 0.77 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2362 1.34 - 1.46: 1549 1.46 - 1.58: 3505 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 7504 Sorted by residual: bond pdb=" C THR B 29 " pdb=" O THR B 29 " ideal model delta sigma weight residual 1.234 1.285 -0.051 1.26e-02 6.30e+03 1.62e+01 bond pdb=" N THR B 34 " pdb=" CA THR B 34 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.32e-02 5.74e+03 1.08e+01 bond pdb=" N ILE B 33 " pdb=" CA ILE B 33 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.26e-02 6.30e+03 8.78e+00 bond pdb=" CA SER R 80 " pdb=" CB SER R 80 " ideal model delta sigma weight residual 1.529 1.483 0.046 1.55e-02 4.16e+03 8.68e+00 bond pdb=" N THR B 29 " pdb=" CA THR B 29 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.27e-02 6.20e+03 7.98e+00 ... (remaining 7499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 9921 2.05 - 4.09: 207 4.09 - 6.14: 22 6.14 - 8.18: 1 8.18 - 10.23: 3 Bond angle restraints: 10154 Sorted by residual: angle pdb=" N GLU B 172 " pdb=" CA GLU B 172 " pdb=" C GLU B 172 " ideal model delta sigma weight residual 114.75 108.11 6.64 1.26e+00 6.30e-01 2.77e+01 angle pdb=" CB ARG B 19 " pdb=" CG ARG B 19 " pdb=" CD ARG B 19 " ideal model delta sigma weight residual 111.30 121.53 -10.23 2.30e+00 1.89e-01 1.98e+01 angle pdb=" N ILE B 171 " pdb=" CA ILE B 171 " pdb=" C ILE B 171 " ideal model delta sigma weight residual 106.21 110.52 -4.31 1.07e+00 8.73e-01 1.62e+01 angle pdb=" N TYR R 294 " pdb=" CA TYR R 294 " pdb=" C TYR R 294 " ideal model delta sigma weight residual 111.07 106.90 4.17 1.07e+00 8.73e-01 1.52e+01 angle pdb=" N SER R 80 " pdb=" CA SER R 80 " pdb=" C SER R 80 " ideal model delta sigma weight residual 111.07 106.96 4.11 1.07e+00 8.73e-01 1.48e+01 ... (remaining 10149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4027 17.73 - 35.46: 352 35.46 - 53.19: 71 53.19 - 70.93: 19 70.93 - 88.66: 6 Dihedral angle restraints: 4475 sinusoidal: 1778 harmonic: 2697 Sorted by residual: dihedral pdb=" CA LEU R 75 " pdb=" C LEU R 75 " pdb=" N VAL R 76 " pdb=" CA VAL R 76 " ideal model delta harmonic sigma weight residual 180.00 -160.99 -19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ARG A 231 " pdb=" C ARG A 231 " pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta harmonic sigma weight residual 180.00 161.37 18.63 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ILE B 171 " pdb=" C ILE B 171 " pdb=" N GLU B 172 " pdb=" CA GLU B 172 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 4472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 848 0.045 - 0.091: 246 0.091 - 0.136: 43 0.136 - 0.182: 1 0.182 - 0.227: 1 Chirality restraints: 1139 Sorted by residual: chirality pdb=" CA MET R 77 " pdb=" N MET R 77 " pdb=" C MET R 77 " pdb=" CB MET R 77 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE B 338 " pdb=" CA ILE B 338 " pdb=" CG1 ILE B 338 " pdb=" CG2 ILE B 338 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1136 not shown) Planarity restraints: 1282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 28 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C ALA B 28 " 0.063 2.00e-02 2.50e+03 pdb=" O ALA B 28 " -0.024 2.00e-02 2.50e+03 pdb=" N THR B 29 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 220 " 0.011 2.00e-02 2.50e+03 1.63e-02 3.97e+00 pdb=" CG HIS A 220 " -0.034 2.00e-02 2.50e+03 pdb=" ND1 HIS A 220 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS A 220 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 HIS A 220 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 220 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " 0.018 2.00e-02 2.50e+03 1.25e-02 3.92e+00 pdb=" CG TRP B 99 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " 0.006 2.00e-02 2.50e+03 ... (remaining 1279 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1628 2.79 - 3.31: 7023 3.31 - 3.84: 11160 3.84 - 4.37: 12677 4.37 - 4.90: 22564 Nonbonded interactions: 55052 Sorted by model distance: nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.257 3.040 nonbonded pdb=" OD1 ASP A 274 " pdb=" ND2 ASN A 278 " model vdw 2.336 3.120 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.348 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.356 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.365 3.040 ... (remaining 55047 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.280 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 6.550 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.003 0.051 7505 Z= 0.194 Angle : 0.690 10.227 10156 Z= 0.423 Chirality : 0.042 0.227 1139 Planarity : 0.004 0.037 1282 Dihedral : 14.264 88.658 2724 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.25 % Allowed : 0.75 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.28), residues: 910 helix: 1.96 (0.26), residues: 394 sheet: -2.04 (0.42), residues: 162 loop : -2.47 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 19 TYR 0.016 0.001 TYR A 253 PHE 0.020 0.001 PHE A 315 TRP 0.033 0.001 TRP B 99 HIS 0.021 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 7504) covalent geometry : angle 0.68997 (10154) SS BOND : bond 0.00479 ( 1) SS BOND : angle 1.08763 ( 2) hydrogen bonds : bond 0.19401 ( 361) hydrogen bonds : angle 6.24240 ( 1050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.280 Fit side-chains REVERT: A 215 ASP cc_start: 0.7936 (t70) cc_final: 0.7588 (t0) REVERT: B 29 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7911 (p) REVERT: B 325 MET cc_start: 0.8455 (mtt) cc_final: 0.8169 (mtm) REVERT: R 162 GLU cc_start: 0.8875 (pt0) cc_final: 0.8674 (pm20) REVERT: R 302 MET cc_start: 0.8018 (mtm) cc_final: 0.7401 (tmm) outliers start: 2 outliers final: 0 residues processed: 134 average time/residue: 0.0808 time to fit residues: 14.9953 Evaluate side-chains 114 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0050 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.186517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144077 restraints weight = 9202.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.142067 restraints weight = 7270.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.143870 restraints weight = 8123.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.144859 restraints weight = 4884.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145577 restraints weight = 4428.242| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7505 Z= 0.146 Angle : 0.596 9.211 10156 Z= 0.315 Chirality : 0.043 0.170 1139 Planarity : 0.004 0.046 1282 Dihedral : 4.474 40.330 1018 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.26 % Allowed : 10.05 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.28), residues: 910 helix: 2.06 (0.26), residues: 397 sheet: -1.85 (0.41), residues: 160 loop : -2.22 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.013 0.001 TYR B 264 PHE 0.027 0.002 PHE R 165 TRP 0.020 0.001 TRP B 82 HIS 0.016 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7504) covalent geometry : angle 0.59596 (10154) SS BOND : bond 0.00187 ( 1) SS BOND : angle 1.35903 ( 2) hydrogen bonds : bond 0.05286 ( 361) hydrogen bonds : angle 4.69298 ( 1050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.308 Fit side-chains REVERT: A 252 SER cc_start: 0.9251 (t) cc_final: 0.9009 (p) REVERT: B 36 ASN cc_start: 0.8625 (p0) cc_final: 0.8363 (p0) REVERT: B 325 MET cc_start: 0.8240 (mtt) cc_final: 0.8027 (mtm) REVERT: R 27 TYR cc_start: 0.8599 (m-80) cc_final: 0.8266 (m-80) outliers start: 10 outliers final: 7 residues processed: 129 average time/residue: 0.0779 time to fit residues: 14.1837 Evaluate side-chains 114 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 295 LEU Chi-restraints excluded: chain R residue 303 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 44 optimal weight: 0.4980 chunk 57 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.183290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.140888 restraints weight = 9039.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138881 restraints weight = 7616.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140231 restraints weight = 8770.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.141413 restraints weight = 4976.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.142226 restraints weight = 4424.243| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7505 Z= 0.163 Angle : 0.589 9.523 10156 Z= 0.311 Chirality : 0.043 0.147 1139 Planarity : 0.004 0.039 1282 Dihedral : 4.323 36.490 1018 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.88 % Allowed : 12.81 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.28), residues: 910 helix: 2.02 (0.25), residues: 398 sheet: -1.84 (0.40), residues: 166 loop : -2.28 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.016 0.001 TYR A 253 PHE 0.023 0.002 PHE R 165 TRP 0.015 0.001 TRP B 82 HIS 0.013 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 7504) covalent geometry : angle 0.58860 (10154) SS BOND : bond 0.00298 ( 1) SS BOND : angle 1.78322 ( 2) hydrogen bonds : bond 0.05507 ( 361) hydrogen bonds : angle 4.46640 ( 1050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: B 36 ASN cc_start: 0.8649 (p0) cc_final: 0.8431 (p0) REVERT: B 75 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7588 (mt0) REVERT: B 325 MET cc_start: 0.8250 (mtt) cc_final: 0.8027 (mtm) REVERT: R 27 TYR cc_start: 0.8598 (m-80) cc_final: 0.8289 (m-80) REVERT: R 257 MET cc_start: 0.8172 (mmm) cc_final: 0.7731 (mmt) REVERT: R 302 MET cc_start: 0.6835 (tmm) cc_final: 0.6517 (tmm) outliers start: 15 outliers final: 9 residues processed: 130 average time/residue: 0.0675 time to fit residues: 12.1861 Evaluate side-chains 116 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 59 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.181161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127546 restraints weight = 9214.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.128518 restraints weight = 5107.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130651 restraints weight = 4306.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.131391 restraints weight = 3970.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.131450 restraints weight = 3624.237| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7505 Z= 0.132 Angle : 0.553 12.054 10156 Z= 0.290 Chirality : 0.042 0.153 1139 Planarity : 0.003 0.039 1282 Dihedral : 4.132 34.278 1017 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.88 % Allowed : 15.20 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.28), residues: 910 helix: 2.05 (0.26), residues: 403 sheet: -1.73 (0.40), residues: 166 loop : -2.15 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 356 TYR 0.017 0.001 TYR A 253 PHE 0.027 0.001 PHE R 154 TRP 0.018 0.001 TRP B 82 HIS 0.010 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7504) covalent geometry : angle 0.55300 (10154) SS BOND : bond 0.00282 ( 1) SS BOND : angle 1.34667 ( 2) hydrogen bonds : bond 0.04959 ( 361) hydrogen bonds : angle 4.25989 ( 1050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 252 SER cc_start: 0.9281 (p) cc_final: 0.9037 (t) REVERT: B 234 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7978 (m-80) REVERT: B 259 GLN cc_start: 0.8635 (tt0) cc_final: 0.8386 (tt0) REVERT: R 27 TYR cc_start: 0.8890 (m-80) cc_final: 0.8314 (m-80) REVERT: R 196 MET cc_start: 0.8932 (mmt) cc_final: 0.8616 (mmm) REVERT: R 302 MET cc_start: 0.6833 (tmm) cc_final: 0.6555 (tmm) outliers start: 15 outliers final: 11 residues processed: 124 average time/residue: 0.0682 time to fit residues: 11.7895 Evaluate side-chains 116 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.184723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.142635 restraints weight = 9011.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141643 restraints weight = 7133.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142557 restraints weight = 8265.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.143590 restraints weight = 4826.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.144500 restraints weight = 4290.306| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7505 Z= 0.132 Angle : 0.548 11.861 10156 Z= 0.287 Chirality : 0.042 0.162 1139 Planarity : 0.003 0.038 1282 Dihedral : 4.077 32.718 1017 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.51 % Allowed : 16.21 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.28), residues: 910 helix: 2.05 (0.25), residues: 404 sheet: -1.54 (0.40), residues: 162 loop : -2.07 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.018 0.001 TYR A 253 PHE 0.030 0.001 PHE R 165 TRP 0.017 0.001 TRP B 82 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7504) covalent geometry : angle 0.54813 (10154) SS BOND : bond 0.00246 ( 1) SS BOND : angle 1.27228 ( 2) hydrogen bonds : bond 0.04871 ( 361) hydrogen bonds : angle 4.16648 ( 1050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.203 Fit side-chains REVERT: A 221 MET cc_start: 0.8336 (ttp) cc_final: 0.8119 (ttp) REVERT: A 252 SER cc_start: 0.9254 (p) cc_final: 0.9022 (t) REVERT: A 317 ARG cc_start: 0.8772 (mpp-170) cc_final: 0.7984 (mpp-170) REVERT: R 27 TYR cc_start: 0.8779 (m-80) cc_final: 0.8242 (m-80) REVERT: R 302 MET cc_start: 0.6918 (tmm) cc_final: 0.6677 (tmm) outliers start: 20 outliers final: 16 residues processed: 126 average time/residue: 0.0636 time to fit residues: 11.1858 Evaluate side-chains 120 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 0.0020 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.184185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.141707 restraints weight = 9122.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.141377 restraints weight = 8346.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143042 restraints weight = 8460.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.143823 restraints weight = 5064.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.145240 restraints weight = 4621.734| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7505 Z= 0.130 Angle : 0.548 11.660 10156 Z= 0.286 Chirality : 0.042 0.172 1139 Planarity : 0.003 0.038 1282 Dihedral : 4.035 31.556 1017 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.01 % Allowed : 17.21 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.28), residues: 910 helix: 2.11 (0.25), residues: 404 sheet: -1.51 (0.40), residues: 164 loop : -2.01 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 22 TYR 0.020 0.001 TYR A 253 PHE 0.035 0.002 PHE R 154 TRP 0.021 0.001 TRP B 339 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7504) covalent geometry : angle 0.54767 (10154) SS BOND : bond 0.00203 ( 1) SS BOND : angle 1.12669 ( 2) hydrogen bonds : bond 0.04735 ( 361) hydrogen bonds : angle 4.12269 ( 1050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.325 Fit side-chains REVERT: A 221 MET cc_start: 0.8415 (ttp) cc_final: 0.8130 (ttp) REVERT: A 252 SER cc_start: 0.9262 (p) cc_final: 0.9039 (t) REVERT: A 317 ARG cc_start: 0.8744 (mpp-170) cc_final: 0.8078 (mpp-170) REVERT: R 27 TYR cc_start: 0.8694 (m-80) cc_final: 0.8224 (m-80) REVERT: R 302 MET cc_start: 0.6936 (tmm) cc_final: 0.6680 (tmm) outliers start: 16 outliers final: 13 residues processed: 119 average time/residue: 0.0682 time to fit residues: 11.3519 Evaluate side-chains 118 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 70 optimal weight: 0.0470 chunk 73 optimal weight: 6.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.182111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123678 restraints weight = 9209.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.128714 restraints weight = 5483.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.131838 restraints weight = 4141.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133404 restraints weight = 3551.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.133742 restraints weight = 3277.935| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 7505 Z= 0.112 Angle : 0.539 12.544 10156 Z= 0.279 Chirality : 0.041 0.185 1139 Planarity : 0.003 0.038 1282 Dihedral : 3.980 29.255 1017 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.01 % Allowed : 17.96 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.28), residues: 910 helix: 2.17 (0.26), residues: 404 sheet: -1.28 (0.40), residues: 162 loop : -1.95 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.019 0.001 TYR A 253 PHE 0.032 0.001 PHE R 165 TRP 0.017 0.001 TRP B 82 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 7504) covalent geometry : angle 0.53861 (10154) SS BOND : bond 0.00186 ( 1) SS BOND : angle 0.81764 ( 2) hydrogen bonds : bond 0.04349 ( 361) hydrogen bonds : angle 4.01932 ( 1050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.206 Fit side-chains REVERT: A 221 MET cc_start: 0.8430 (ttp) cc_final: 0.8188 (ttp) REVERT: A 252 SER cc_start: 0.9215 (p) cc_final: 0.8984 (t) REVERT: A 317 ARG cc_start: 0.8827 (mpp-170) cc_final: 0.8085 (mpp-170) REVERT: B 175 GLN cc_start: 0.8450 (mt0) cc_final: 0.7986 (mm-40) REVERT: R 27 TYR cc_start: 0.8841 (m-80) cc_final: 0.8289 (m-80) outliers start: 16 outliers final: 13 residues processed: 123 average time/residue: 0.0672 time to fit residues: 11.5491 Evaluate side-chains 121 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 149 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 88 ASN B 259 GLN R 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.182670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.139924 restraints weight = 9203.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.137913 restraints weight = 7482.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.139578 restraints weight = 8594.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.140741 restraints weight = 5382.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.145009 restraints weight = 4821.537| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7505 Z= 0.150 Angle : 0.570 12.341 10156 Z= 0.298 Chirality : 0.042 0.177 1139 Planarity : 0.003 0.035 1282 Dihedral : 4.027 29.181 1017 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.01 % Allowed : 18.47 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.28), residues: 910 helix: 2.19 (0.25), residues: 398 sheet: -1.28 (0.41), residues: 164 loop : -1.93 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.010 0.001 TYR A 311 PHE 0.036 0.002 PHE R 154 TRP 0.019 0.001 TRP B 339 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 7504) covalent geometry : angle 0.57012 (10154) SS BOND : bond 0.00197 ( 1) SS BOND : angle 1.36850 ( 2) hydrogen bonds : bond 0.05048 ( 361) hydrogen bonds : angle 4.13401 ( 1050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.297 Fit side-chains REVERT: A 221 MET cc_start: 0.8443 (ttp) cc_final: 0.8204 (ttp) REVERT: A 317 ARG cc_start: 0.8782 (mpp-170) cc_final: 0.8061 (mpp-170) REVERT: B 175 GLN cc_start: 0.8455 (mt0) cc_final: 0.8055 (mm-40) REVERT: R 27 TYR cc_start: 0.8781 (m-80) cc_final: 0.8246 (m-80) outliers start: 16 outliers final: 12 residues processed: 118 average time/residue: 0.0808 time to fit residues: 13.2323 Evaluate side-chains 117 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 67 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.180831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137887 restraints weight = 8916.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.137578 restraints weight = 8393.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.138280 restraints weight = 9796.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.139548 restraints weight = 5645.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.140120 restraints weight = 4933.665| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7505 Z= 0.178 Angle : 0.599 12.401 10156 Z= 0.316 Chirality : 0.043 0.179 1139 Planarity : 0.004 0.035 1282 Dihedral : 4.167 28.589 1017 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.88 % Allowed : 18.47 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.28), residues: 910 helix: 2.08 (0.25), residues: 398 sheet: -1.32 (0.41), residues: 166 loop : -1.93 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.019 0.001 TYR A 253 PHE 0.033 0.002 PHE R 154 TRP 0.018 0.002 TRP B 339 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 7504) covalent geometry : angle 0.59911 (10154) SS BOND : bond 0.00159 ( 1) SS BOND : angle 1.48168 ( 2) hydrogen bonds : bond 0.05551 ( 361) hydrogen bonds : angle 4.24322 ( 1050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.288 Fit side-chains REVERT: A 208 PHE cc_start: 0.7057 (m-10) cc_final: 0.6852 (m-10) REVERT: A 221 MET cc_start: 0.8430 (ttp) cc_final: 0.8153 (ttp) REVERT: A 317 ARG cc_start: 0.8702 (mpp-170) cc_final: 0.8064 (mpp-170) REVERT: R 27 TYR cc_start: 0.8632 (m-80) cc_final: 0.8177 (m-80) outliers start: 15 outliers final: 14 residues processed: 114 average time/residue: 0.0691 time to fit residues: 10.9289 Evaluate side-chains 117 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 57 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 0.0470 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.180824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.138821 restraints weight = 9047.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.135737 restraints weight = 8332.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137626 restraints weight = 9999.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.138866 restraints weight = 5926.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.139643 restraints weight = 5251.808| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 7505 Z= 0.213 Angle : 0.963 59.200 10156 Z= 0.558 Chirality : 0.045 0.513 1139 Planarity : 0.004 0.084 1282 Dihedral : 4.237 28.618 1017 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.62 % Favored : 95.27 % Rotamer: Outliers : 1.88 % Allowed : 19.10 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.28), residues: 910 helix: 2.09 (0.25), residues: 398 sheet: -1.33 (0.41), residues: 166 loop : -1.95 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG B 19 TYR 0.020 0.001 TYR A 253 PHE 0.032 0.002 PHE R 154 TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 7504) covalent geometry : angle 0.96305 (10154) SS BOND : bond 0.00245 ( 1) SS BOND : angle 1.47281 ( 2) hydrogen bonds : bond 0.05494 ( 361) hydrogen bonds : angle 4.24297 ( 1050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.306 Fit side-chains REVERT: A 208 PHE cc_start: 0.7079 (m-10) cc_final: 0.6862 (m-10) REVERT: A 221 MET cc_start: 0.8412 (ttp) cc_final: 0.8155 (ttp) REVERT: A 317 ARG cc_start: 0.8722 (mpp-170) cc_final: 0.8068 (mpp-170) REVERT: R 27 TYR cc_start: 0.8658 (m-80) cc_final: 0.8187 (m-80) outliers start: 15 outliers final: 13 residues processed: 113 average time/residue: 0.0701 time to fit residues: 11.0743 Evaluate side-chains 116 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 88 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 0.0030 chunk 89 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.181064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139021 restraints weight = 9000.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.136744 restraints weight = 8307.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.138217 restraints weight = 9612.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139605 restraints weight = 5540.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.140398 restraints weight = 4824.718| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 7505 Z= 0.213 Angle : 0.963 59.200 10156 Z= 0.558 Chirality : 0.045 0.513 1139 Planarity : 0.004 0.084 1282 Dihedral : 4.237 28.618 1017 Min Nonbonded Distance : 1.557 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.62 % Favored : 95.27 % Rotamer: Outliers : 1.76 % Allowed : 19.35 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.28), residues: 910 helix: 2.09 (0.25), residues: 398 sheet: -1.33 (0.41), residues: 166 loop : -1.95 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG B 19 TYR 0.020 0.001 TYR A 253 PHE 0.032 0.002 PHE R 154 TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 7504) covalent geometry : angle 0.96305 (10154) SS BOND : bond 0.00245 ( 1) SS BOND : angle 1.47281 ( 2) hydrogen bonds : bond 0.05494 ( 361) hydrogen bonds : angle 4.24297 ( 1050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1204.92 seconds wall clock time: 21 minutes 30.27 seconds (1290.27 seconds total)