Starting phenix.real_space_refine on Sun Apr 5 01:15:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zfo_74146/04_2026/9zfo_74146.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zfo_74146/04_2026/9zfo_74146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zfo_74146/04_2026/9zfo_74146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zfo_74146/04_2026/9zfo_74146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zfo_74146/04_2026/9zfo_74146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zfo_74146/04_2026/9zfo_74146.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 36 5.16 5 C 4257 2.51 5 N 1150 2.21 5 O 1192 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-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6635 Number of models: 1 Model: "" Number of chains: 3 Chain: "U" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2421 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 11, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "S" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3611 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 420} Chain breaks: 8 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 603 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 73} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 1.51, per 1000 atoms: 0.23 Number of scatterers: 6635 At special positions: 0 Unit cell: (78, 87.75, 134.25, 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 36 16.00 O 1192 8.00 N 1150 7.00 C 4257 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: 0.46 Conformation dependent library (CDL) restraints added in 231.2 milliseconds 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 43.3% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'U' and resid 63 through 76 removed outlier: 3.551A pdb=" N GLN U 71 " --> pdb=" O ASN U 67 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL U 72 " --> pdb=" O SER U 68 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN U 76 " --> pdb=" O VAL U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 84 removed outlier: 3.601A pdb=" N ILE U 82 " --> pdb=" O ASP U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 91 through 97 Processing helix chain 'U' and resid 98 through 112 removed outlier: 3.701A pdb=" N ASP U 112 " --> pdb=" O GLU U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 120 through 129 removed outlier: 3.503A pdb=" N ALA U 124 " --> pdb=" O PRO U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 139 through 154 Processing helix chain 'U' and resid 157 through 168 removed outlier: 3.869A pdb=" N VAL U 161 " --> pdb=" O ASP U 157 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG U 163 " --> pdb=" O HIS U 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 211 through 218 Processing helix chain 'U' and resid 343 through 349 removed outlier: 3.738A pdb=" N ILE U 347 " --> pdb=" O SER U 343 " (cutoff:3.500A) Processing helix chain 'U' and resid 350 through 352 No H-bonds generated for 'chain 'U' and resid 350 through 352' Processing helix chain 'S' and resid 143 through 172 Processing helix chain 'S' and resid 199 through 249 Proline residue: S 233 - end of helix Processing helix chain 'S' and resid 255 through 283 removed outlier: 3.717A pdb=" N THR S 260 " --> pdb=" O GLU S 256 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP S 261 " --> pdb=" O GLN S 257 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU S 268 " --> pdb=" O ALA S 264 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU S 269 " --> pdb=" O GLY S 265 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN S 274 " --> pdb=" O PHE S 270 " (cutoff:3.500A) Processing helix chain 'S' and resid 292 through 314 removed outlier: 4.628A pdb=" N VAL S 297 " --> pdb=" O LEU S 293 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG S 300 " --> pdb=" O GLY S 296 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA S 302 " --> pdb=" O ASP S 298 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN S 303 " --> pdb=" O LEU S 299 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU S 306 " --> pdb=" O ALA S 302 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG S 314 " --> pdb=" O ARG S 310 " (cutoff:3.500A) Processing helix chain 'S' and resid 458 through 460 No H-bonds generated for 'chain 'S' and resid 458 through 460' Processing helix chain 'S' and resid 461 through 474 removed outlier: 3.959A pdb=" N LEU S 474 " --> pdb=" O LEU S 470 " (cutoff:3.500A) Processing helix chain 'S' and resid 492 through 508 Proline residue: S 498 - end of helix removed outlier: 3.965A pdb=" N GLN S 503 " --> pdb=" O ALA S 499 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE S 504 " --> pdb=" O LEU S 500 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL S 508 " --> pdb=" O PHE S 504 " (cutoff:3.500A) Processing helix chain 'S' and resid 513 through 526 removed outlier: 3.524A pdb=" N LEU S 517 " --> pdb=" O ASN S 513 " (cutoff:3.500A) Processing helix chain 'S' and resid 537 through 543 removed outlier: 3.690A pdb=" N THR S 542 " --> pdb=" O TRP S 538 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS S 543 " --> pdb=" O ALA S 539 " (cutoff:3.500A) Processing helix chain 'S' and resid 552 through 567 removed outlier: 3.556A pdb=" N ASP S 566 " --> pdb=" O GLU S 562 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS S 567 " --> pdb=" O LEU S 563 " (cutoff:3.500A) Processing helix chain 'S' and resid 568 through 574 Processing helix chain 'S' and resid 582 through 591 Processing helix chain 'S' and resid 632 through 637 removed outlier: 3.542A pdb=" N GLN S 637 " --> pdb=" O LYS S 633 " (cutoff:3.500A) Processing helix chain 'S' and resid 640 through 647 Processing helix chain 'S' and resid 669 through 676 removed outlier: 3.529A pdb=" N CYS S 676 " --> pdb=" O GLU S 672 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 116 removed outlier: 3.622A pdb=" N LEU I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'U' and resid 56 through 57 removed outlier: 6.319A pdb=" N GLY U 56 " --> pdb=" O VAL U 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'U' and resid 184 through 191 removed outlier: 7.074A pdb=" N ARG U 171 " --> pdb=" O THR U 246 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS U 244 " --> pdb=" O LYS U 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'U' and resid 194 through 197 removed outlier: 5.747A pdb=" N LEU U 194 " --> pdb=" O HIS U 255 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N MET U 257 " --> pdb=" O LEU U 194 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU U 196 " --> pdb=" O MET U 257 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N TYR U 363 " --> pdb=" O LEU U 256 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLU U 360 " --> pdb=" O GLY U 312 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLY U 312 " --> pdb=" O GLU U 360 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA U 362 " --> pdb=" O HIS U 310 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N HIS U 310 " --> pdb=" O ALA U 362 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N MET U 368 " --> pdb=" O LEU U 304 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU U 304 " --> pdb=" O MET U 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'U' and resid 194 through 197 removed outlier: 5.747A pdb=" N LEU U 194 " --> pdb=" O HIS U 255 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N MET U 257 " --> pdb=" O LEU U 194 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU U 196 " --> pdb=" O MET U 257 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N TYR U 363 " --> pdb=" O LEU U 256 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLU U 360 " --> pdb=" O GLY U 312 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLY U 312 " --> pdb=" O GLU U 360 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA U 362 " --> pdb=" O HIS U 310 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N HIS U 310 " --> pdb=" O ALA U 362 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N MET U 368 " --> pdb=" O LEU U 304 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU U 304 " --> pdb=" O MET U 368 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE U 305 " --> pdb=" O ARG U 324 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL U 311 " --> pdb=" O HIS U 318 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL U 321 " --> pdb=" O PHE U 334 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP U 331 " --> pdb=" O VAL U 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'U' and resid 260 through 261 Processing sheet with id=AA6, first strand: chain 'S' and resid 316 through 323 removed outlier: 6.497A pdb=" N ARG S 343 " --> pdb=" O GLU S 319 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLN S 321 " --> pdb=" O THR S 341 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N THR S 341 " --> pdb=" O GLN S 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 333 through 335 removed outlier: 6.664A pdb=" N LEU S 334 " --> pdb=" O ILE S 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'S' and resid 362 through 363 removed outlier: 3.629A pdb=" N TYR S 439 " --> pdb=" O LEU S 442 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU S 442 " --> pdb=" O TYR S 439 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 600 through 602 Processing sheet with id=AB1, first strand: chain 'I' and resid 95 through 98 removed outlier: 9.073A pdb=" N VAL I 148 " --> pdb=" O SER I 83 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU I 85 " --> pdb=" O VAL I 148 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N MET I 150 " --> pdb=" O LEU I 85 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG I 87 " --> pdb=" O MET I 150 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N LEU I 152 " --> pdb=" O ARG I 87 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 861 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: 1.00 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2112 1.34 - 1.46: 1462 1.46 - 1.58: 3143 1.58 - 1.70: 0 1.70 - 1.82: 52 Bond restraints: 6769 Sorted by residual: bond pdb=" CA LEU S 232 " pdb=" C LEU S 232 " ideal model delta sigma weight residual 1.524 1.551 -0.028 1.26e-02 6.30e+03 4.81e+00 bond pdb=" C PRO S 547 " pdb=" N PRO S 548 " ideal model delta sigma weight residual 1.334 1.375 -0.042 2.34e-02 1.83e+03 3.16e+00 bond pdb=" C LEU S 232 " pdb=" N PRO S 233 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.28e-02 6.10e+03 2.76e+00 bond pdb=" C VAL U 99 " pdb=" N PRO U 100 " ideal model delta sigma weight residual 1.336 1.355 -0.020 1.23e-02 6.61e+03 2.62e+00 bond pdb=" CB GLU U 210 " pdb=" CG GLU U 210 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.48e+00 ... (remaining 6764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 8950 2.79 - 5.58: 168 5.58 - 8.38: 32 8.38 - 11.17: 6 11.17 - 13.96: 3 Bond angle restraints: 9159 Sorted by residual: angle pdb=" CA ILE S 149 " pdb=" CB ILE S 149 " pdb=" CG2 ILE S 149 " ideal model delta sigma weight residual 110.50 118.48 -7.98 1.70e+00 3.46e-01 2.20e+01 angle pdb=" CB MET S 519 " pdb=" CG MET S 519 " pdb=" SD MET S 519 " ideal model delta sigma weight residual 112.70 126.66 -13.96 3.00e+00 1.11e-01 2.17e+01 angle pdb=" CB MET S 594 " pdb=" CG MET S 594 " pdb=" SD MET S 594 " ideal model delta sigma weight residual 112.70 126.18 -13.48 3.00e+00 1.11e-01 2.02e+01 angle pdb=" C LEU S 152 " pdb=" N ARG S 153 " pdb=" CA ARG S 153 " ideal model delta sigma weight residual 122.06 114.05 8.01 1.86e+00 2.89e-01 1.85e+01 angle pdb=" N GLU S 146 " pdb=" CA GLU S 146 " pdb=" CB GLU S 146 " ideal model delta sigma weight residual 110.28 116.93 -6.65 1.55e+00 4.16e-01 1.84e+01 ... (remaining 9154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 3690 17.91 - 35.82: 347 35.82 - 53.72: 51 53.72 - 71.63: 7 71.63 - 89.54: 2 Dihedral angle restraints: 4097 sinusoidal: 1689 harmonic: 2408 Sorted by residual: dihedral pdb=" CA ARG S 330 " pdb=" C ARG S 330 " pdb=" N PRO S 331 " pdb=" CA PRO S 331 " ideal model delta harmonic sigma weight residual -180.00 -153.65 -26.35 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA LEU S 293 " pdb=" C LEU S 293 " pdb=" N THR S 294 " pdb=" CA THR S 294 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA ASN U 335 " pdb=" C ASN U 335 " pdb=" N ASP U 336 " pdb=" CA ASP U 336 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 4094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 764 0.048 - 0.095: 202 0.095 - 0.143: 64 0.143 - 0.191: 13 0.191 - 0.239: 6 Chirality restraints: 1049 Sorted by residual: chirality pdb=" CA ARG S 153 " pdb=" N ARG S 153 " pdb=" C ARG S 153 " pdb=" CB ARG S 153 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB ILE S 149 " pdb=" CA ILE S 149 " pdb=" CG1 ILE S 149 " pdb=" CG2 ILE S 149 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE U 177 " pdb=" CA ILE U 177 " pdb=" CG1 ILE U 177 " pdb=" CG2 ILE U 177 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1046 not shown) Planarity restraints: 1154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE S 149 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C ILE S 149 " 0.068 2.00e-02 2.50e+03 pdb=" O ILE S 149 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU S 150 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU S 232 " 0.059 5.00e-02 4.00e+02 8.85e-02 1.25e+01 pdb=" N PRO S 233 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO S 233 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO S 233 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO S 547 " -0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO S 548 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO S 548 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO S 548 " -0.047 5.00e-02 4.00e+02 ... (remaining 1151 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1616 2.80 - 3.33: 5554 3.33 - 3.85: 10392 3.85 - 4.38: 11797 4.38 - 4.90: 21037 Nonbonded interactions: 50396 Sorted by model distance: nonbonded pdb=" O LEU S 350 " pdb=" OH TYR S 437 " model vdw 2.280 3.040 nonbonded pdb=" OG SER U 278 " pdb=" OE1 GLN U 301 " model vdw 2.291 3.040 nonbonded pdb=" OG SER I 112 " pdb=" OD1 ASP I 119 " model vdw 2.344 3.040 nonbonded pdb=" O LEU U 145 " pdb=" ND2 ASN U 149 " model vdw 2.364 3.120 nonbonded pdb=" OD1 ASN S 528 " pdb=" OG1 THR S 531 " model vdw 2.377 3.040 ... (remaining 50391 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 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: 3.510 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.560 Find NCS groups from input model: 0.020 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 : 0.005 0.049 6769 Z= 0.219 Angle : 0.962 13.961 9159 Z= 0.477 Chirality : 0.052 0.239 1049 Planarity : 0.009 0.088 1154 Dihedral : 13.490 89.539 2525 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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 are not related in a simple way. whole: -2.65 (0.26), residues: 803 helix: -1.70 (0.23), residues: 334 sheet: -0.49 (0.48), residues: 123 loop : -2.20 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG S 248 TYR 0.020 0.002 TYR U 144 PHE 0.030 0.003 PHE S 270 TRP 0.011 0.002 TRP S 554 HIS 0.006 0.001 HIS U 271 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 6769) covalent geometry : angle 0.96154 ( 9159) hydrogen bonds : bond 0.17659 ( 286) hydrogen bonds : angle 7.74456 ( 861) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: U 183 MET cc_start: 0.6949 (tpt) cc_final: 0.6338 (mtt) REVERT: U 313 MET cc_start: 0.8161 (tpp) cc_final: 0.7727 (mtp) REVERT: S 515 ASP cc_start: 0.6921 (m-30) cc_final: 0.5923 (t0) REVERT: I 112 SER cc_start: 0.7037 (m) cc_final: 0.6768 (m) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0974 time to fit residues: 8.3343 Evaluate side-chains 49 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 165 GLN ** U 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN S 271 HIS S 377 ASN I 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.187633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.136768 restraints weight = 7011.562| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.48 r_work: 0.3566 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 6769 Z= 0.316 Angle : 0.832 9.365 9159 Z= 0.423 Chirality : 0.050 0.260 1049 Planarity : 0.007 0.072 1154 Dihedral : 5.502 21.557 883 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.23 % Favored : 93.65 % Rotamer: Outliers : 1.35 % Allowed : 7.31 % Favored : 91.34 % 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 are not related in a simple way. whole: -1.87 (0.27), residues: 803 helix: -0.83 (0.26), residues: 330 sheet: 0.22 (0.51), residues: 105 loop : -2.05 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 273 TYR 0.018 0.003 TYR S 507 PHE 0.021 0.003 PHE S 373 TRP 0.017 0.002 TRP S 554 HIS 0.010 0.002 HIS U 271 Details of bonding type rmsd covalent geometry : bond 0.00781 ( 6769) covalent geometry : angle 0.83220 ( 9159) hydrogen bonds : bond 0.07576 ( 286) hydrogen bonds : angle 5.73150 ( 861) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 183 MET cc_start: 0.6894 (tpt) cc_final: 0.6001 (mtp) REVERT: U 192 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8344 (tp) REVERT: U 301 GLN cc_start: 0.7238 (tp-100) cc_final: 0.7014 (tp40) REVERT: U 339 ILE cc_start: 0.7922 (mm) cc_final: 0.7645 (mm) REVERT: S 155 MET cc_start: 0.6416 (mpp) cc_final: 0.5764 (mpp) REVERT: S 229 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6414 (mp0) REVERT: S 339 LYS cc_start: 0.7051 (ptmt) cc_final: 0.6495 (ptpp) REVERT: S 462 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6857 (tt) REVERT: S 515 ASP cc_start: 0.7052 (m-30) cc_final: 0.6075 (t0) REVERT: S 578 MET cc_start: 0.6628 (ppp) cc_final: 0.6407 (ppp) REVERT: I 120 ASP cc_start: 0.7754 (m-30) cc_final: 0.7501 (m-30) REVERT: I 155 ARG cc_start: 0.8916 (mtp85) cc_final: 0.8465 (mtt90) outliers start: 10 outliers final: 2 residues processed: 81 average time/residue: 0.0988 time to fit residues: 10.5019 Evaluate side-chains 64 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 189 SER Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain S residue 229 GLU Chi-restraints excluded: chain S residue 462 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.193295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.143539 restraints weight = 6805.158| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.50 r_work: 0.3617 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6769 Z= 0.147 Angle : 0.600 7.997 9159 Z= 0.309 Chirality : 0.041 0.184 1049 Planarity : 0.006 0.060 1154 Dihedral : 4.883 18.648 883 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.76 % Allowed : 10.42 % Favored : 87.82 % 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 are not related in a simple way. whole: -1.17 (0.29), residues: 803 helix: 0.07 (0.28), residues: 323 sheet: 0.06 (0.51), residues: 112 loop : -1.83 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 97 TYR 0.015 0.001 TYR U 144 PHE 0.013 0.002 PHE U 275 TRP 0.016 0.001 TRP S 554 HIS 0.005 0.001 HIS U 271 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6769) covalent geometry : angle 0.59971 ( 9159) hydrogen bonds : bond 0.05636 ( 286) hydrogen bonds : angle 5.20171 ( 861) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 183 MET cc_start: 0.6791 (tpt) cc_final: 0.5932 (mtt) REVERT: S 155 MET cc_start: 0.6212 (mpp) cc_final: 0.5882 (mpp) REVERT: S 229 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: S 339 LYS cc_start: 0.6880 (ptmt) cc_final: 0.6269 (ptpp) REVERT: S 515 ASP cc_start: 0.6954 (m-30) cc_final: 0.6073 (t0) REVERT: I 120 ASP cc_start: 0.7632 (m-30) cc_final: 0.7403 (m-30) REVERT: I 155 ARG cc_start: 0.8860 (mtp85) cc_final: 0.8358 (mtt90) outliers start: 13 outliers final: 8 residues processed: 72 average time/residue: 0.0942 time to fit residues: 9.0874 Evaluate side-chains 71 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 177 ILE Chi-restraints excluded: chain U residue 189 SER Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 303 GLU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 229 GLU Chi-restraints excluded: chain S residue 436 LYS Chi-restraints excluded: chain S residue 438 THR Chi-restraints excluded: chain S residue 561 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 335 ASN S 142 GLN ** S 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.194966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.144753 restraints weight = 6846.913| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.53 r_work: 0.3630 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6769 Z= 0.135 Angle : 0.568 7.952 9159 Z= 0.293 Chirality : 0.040 0.166 1049 Planarity : 0.005 0.053 1154 Dihedral : 4.601 16.899 883 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.44 % Allowed : 11.23 % Favored : 86.33 % 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 are not related in a simple way. whole: -0.77 (0.29), residues: 803 helix: 0.52 (0.29), residues: 323 sheet: 0.02 (0.49), residues: 118 loop : -1.66 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 97 TYR 0.017 0.001 TYR U 144 PHE 0.011 0.001 PHE U 275 TRP 0.015 0.001 TRP S 554 HIS 0.011 0.001 HIS S 271 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6769) covalent geometry : angle 0.56817 ( 9159) hydrogen bonds : bond 0.05099 ( 286) hydrogen bonds : angle 4.96989 ( 861) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.286 Fit side-chains REVERT: U 183 MET cc_start: 0.6720 (tpt) cc_final: 0.5971 (mtt) REVERT: U 192 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8354 (tp) REVERT: S 155 MET cc_start: 0.5837 (mpp) cc_final: 0.5567 (mpp) REVERT: S 229 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6086 (mp0) REVERT: S 515 ASP cc_start: 0.6870 (m-30) cc_final: 0.6060 (t0) REVERT: S 594 MET cc_start: 0.6059 (mmm) cc_final: 0.5203 (ptt) REVERT: I 82 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6350 (pp) REVERT: I 155 ARG cc_start: 0.8704 (mtp85) cc_final: 0.8164 (mtt90) outliers start: 18 outliers final: 9 residues processed: 76 average time/residue: 0.0928 time to fit residues: 9.5066 Evaluate side-chains 70 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 177 ILE Chi-restraints excluded: chain U residue 189 SER Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain U residue 303 GLU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 229 GLU Chi-restraints excluded: chain S residue 373 PHE Chi-restraints excluded: chain S residue 436 LYS Chi-restraints excluded: chain S residue 438 THR Chi-restraints excluded: chain S residue 462 LEU Chi-restraints excluded: chain S residue 561 LEU Chi-restraints excluded: chain I residue 82 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.192310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141830 restraints weight = 6966.814| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.53 r_work: 0.3595 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6769 Z= 0.158 Angle : 0.587 7.459 9159 Z= 0.301 Chirality : 0.041 0.209 1049 Planarity : 0.005 0.051 1154 Dihedral : 4.582 16.491 883 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.25 % Allowed : 10.55 % Favored : 86.20 % 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 are not related in a simple way. whole: -0.70 (0.29), residues: 803 helix: 0.60 (0.29), residues: 329 sheet: -0.04 (0.49), residues: 118 loop : -1.64 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 97 TYR 0.016 0.001 TYR U 144 PHE 0.012 0.002 PHE U 275 TRP 0.015 0.001 TRP S 554 HIS 0.008 0.001 HIS S 271 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 6769) covalent geometry : angle 0.58715 ( 9159) hydrogen bonds : bond 0.05324 ( 286) hydrogen bonds : angle 4.93570 ( 861) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.251 Fit side-chains REVERT: U 183 MET cc_start: 0.6720 (tpt) cc_final: 0.5980 (mtt) REVERT: U 192 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8378 (tp) REVERT: U 339 ILE cc_start: 0.7808 (mm) cc_final: 0.7543 (mm) REVERT: S 142 GLN cc_start: 0.6541 (tt0) cc_final: 0.6140 (tt0) REVERT: S 155 MET cc_start: 0.5852 (mpp) cc_final: 0.5508 (mpp) REVERT: S 229 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6954 (tt0) REVERT: S 339 LYS cc_start: 0.6851 (ptmt) cc_final: 0.6202 (ptpp) REVERT: S 515 ASP cc_start: 0.6856 (m-30) cc_final: 0.6036 (t0) REVERT: I 82 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6369 (pp) outliers start: 24 outliers final: 13 residues processed: 80 average time/residue: 0.0953 time to fit residues: 10.1608 Evaluate side-chains 74 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 161 VAL Chi-restraints excluded: chain U residue 177 ILE Chi-restraints excluded: chain U residue 189 SER Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain U residue 303 GLU Chi-restraints excluded: chain S residue 153 ARG Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 229 GLU Chi-restraints excluded: chain S residue 373 PHE Chi-restraints excluded: chain S residue 436 LYS Chi-restraints excluded: chain S residue 438 THR Chi-restraints excluded: chain S residue 462 LEU Chi-restraints excluded: chain S residue 561 LEU Chi-restraints excluded: chain I residue 82 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 50 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.193166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.143195 restraints weight = 6950.611| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.46 r_work: 0.3618 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6769 Z= 0.144 Angle : 0.579 8.616 9159 Z= 0.295 Chirality : 0.041 0.197 1049 Planarity : 0.005 0.050 1154 Dihedral : 4.476 15.763 883 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.98 % Allowed : 11.23 % Favored : 85.79 % 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 are not related in a simple way. whole: -0.55 (0.30), residues: 803 helix: 0.77 (0.29), residues: 329 sheet: -0.06 (0.49), residues: 118 loop : -1.57 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 97 TYR 0.015 0.001 TYR U 144 PHE 0.016 0.002 PHE U 217 TRP 0.015 0.001 TRP S 554 HIS 0.006 0.001 HIS S 271 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6769) covalent geometry : angle 0.57859 ( 9159) hydrogen bonds : bond 0.05062 ( 286) hydrogen bonds : angle 4.84546 ( 861) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.403 Fit side-chains REVERT: U 183 MET cc_start: 0.6816 (tpt) cc_final: 0.5900 (mtp) REVERT: U 192 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8399 (tp) REVERT: U 339 ILE cc_start: 0.7793 (mm) cc_final: 0.7485 (mm) REVERT: S 155 MET cc_start: 0.6217 (mpp) cc_final: 0.5781 (mpp) REVERT: S 229 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6412 (mp0) REVERT: S 339 LYS cc_start: 0.6775 (ptmt) cc_final: 0.6148 (ptpp) REVERT: S 515 ASP cc_start: 0.6886 (m-30) cc_final: 0.6076 (t0) REVERT: I 82 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6379 (pp) outliers start: 22 outliers final: 16 residues processed: 75 average time/residue: 0.0981 time to fit residues: 9.7669 Evaluate side-chains 77 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 52 HIS Chi-restraints excluded: chain U residue 161 VAL Chi-restraints excluded: chain U residue 169 THR Chi-restraints excluded: chain U residue 177 ILE Chi-restraints excluded: chain U residue 189 SER Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain U residue 303 GLU Chi-restraints excluded: chain S residue 153 ARG Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 229 GLU Chi-restraints excluded: chain S residue 373 PHE Chi-restraints excluded: chain S residue 436 LYS Chi-restraints excluded: chain S residue 438 THR Chi-restraints excluded: chain S residue 462 LEU Chi-restraints excluded: chain S residue 561 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 120 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 24 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.194502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.145015 restraints weight = 6806.622| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.44 r_work: 0.3639 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6769 Z= 0.125 Angle : 0.561 9.194 9159 Z= 0.284 Chirality : 0.040 0.186 1049 Planarity : 0.005 0.049 1154 Dihedral : 4.325 15.310 883 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.71 % Allowed : 11.37 % Favored : 85.93 % 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 are not related in a simple way. whole: -0.39 (0.30), residues: 803 helix: 0.96 (0.30), residues: 329 sheet: -0.06 (0.49), residues: 118 loop : -1.51 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 97 TYR 0.014 0.001 TYR U 144 PHE 0.013 0.001 PHE S 270 TRP 0.015 0.001 TRP S 554 HIS 0.004 0.001 HIS S 271 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6769) covalent geometry : angle 0.56141 ( 9159) hydrogen bonds : bond 0.04691 ( 286) hydrogen bonds : angle 4.67916 ( 861) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: U 103 MET cc_start: 0.8048 (ttt) cc_final: 0.7660 (ttt) REVERT: U 183 MET cc_start: 0.6703 (tpt) cc_final: 0.5977 (mtt) REVERT: U 339 ILE cc_start: 0.7674 (mm) cc_final: 0.7420 (mm) REVERT: S 155 MET cc_start: 0.5848 (mpp) cc_final: 0.5486 (mpp) REVERT: S 515 ASP cc_start: 0.6843 (m-30) cc_final: 0.6057 (t0) REVERT: I 82 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6359 (pp) outliers start: 20 outliers final: 15 residues processed: 75 average time/residue: 0.1015 time to fit residues: 10.0113 Evaluate side-chains 74 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 161 VAL Chi-restraints excluded: chain U residue 169 THR Chi-restraints excluded: chain U residue 177 ILE Chi-restraints excluded: chain U residue 189 SER Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain U residue 303 GLU Chi-restraints excluded: chain S residue 153 ARG Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 436 LYS Chi-restraints excluded: chain S residue 438 THR Chi-restraints excluded: chain S residue 462 LEU Chi-restraints excluded: chain S residue 561 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 132 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 64 optimal weight: 0.0570 chunk 65 optimal weight: 0.0970 chunk 46 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.196862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.146718 restraints weight = 6949.875| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.54 r_work: 0.3657 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6769 Z= 0.113 Angle : 0.548 10.389 9159 Z= 0.275 Chirality : 0.039 0.171 1049 Planarity : 0.005 0.048 1154 Dihedral : 4.139 14.713 883 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.44 % Allowed : 11.91 % Favored : 85.66 % 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 are not related in a simple way. whole: -0.23 (0.30), residues: 803 helix: 1.14 (0.30), residues: 329 sheet: -0.08 (0.49), residues: 119 loop : -1.44 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 97 TYR 0.008 0.001 TYR U 168 PHE 0.011 0.001 PHE S 270 TRP 0.014 0.001 TRP S 554 HIS 0.004 0.001 HIS U 271 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6769) covalent geometry : angle 0.54757 ( 9159) hydrogen bonds : bond 0.04360 ( 286) hydrogen bonds : angle 4.55836 ( 861) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: U 103 MET cc_start: 0.8052 (ttt) cc_final: 0.7711 (ttt) REVERT: U 183 MET cc_start: 0.6770 (tpt) cc_final: 0.6010 (mtt) REVERT: U 339 ILE cc_start: 0.7637 (mm) cc_final: 0.7379 (mm) REVERT: S 153 ARG cc_start: 0.6845 (mtm-85) cc_final: 0.6351 (mtm-85) REVERT: S 155 MET cc_start: 0.5740 (mpp) cc_final: 0.5412 (mpp) REVERT: S 515 ASP cc_start: 0.6834 (m-30) cc_final: 0.6046 (t0) REVERT: I 82 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6316 (pp) REVERT: I 155 ARG cc_start: 0.8780 (mtp85) cc_final: 0.8512 (mtt90) outliers start: 18 outliers final: 13 residues processed: 77 average time/residue: 0.1050 time to fit residues: 10.5199 Evaluate side-chains 73 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 161 VAL Chi-restraints excluded: chain U residue 169 THR Chi-restraints excluded: chain U residue 177 ILE Chi-restraints excluded: chain U residue 189 SER Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 436 LYS Chi-restraints excluded: chain S residue 438 THR Chi-restraints excluded: chain S residue 462 LEU Chi-restraints excluded: chain S residue 523 LYS Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 132 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 21 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.196036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.145871 restraints weight = 6912.465| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.51 r_work: 0.3647 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6769 Z= 0.121 Angle : 0.558 10.712 9159 Z= 0.280 Chirality : 0.040 0.166 1049 Planarity : 0.005 0.048 1154 Dihedral : 4.144 14.828 883 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.30 % Allowed : 12.58 % Favored : 85.12 % 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 are not related in a simple way. whole: -0.19 (0.30), residues: 803 helix: 1.17 (0.29), residues: 329 sheet: -0.07 (0.49), residues: 119 loop : -1.41 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 97 TYR 0.010 0.001 TYR U 168 PHE 0.012 0.001 PHE S 270 TRP 0.013 0.001 TRP S 554 HIS 0.004 0.001 HIS U 271 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6769) covalent geometry : angle 0.55839 ( 9159) hydrogen bonds : bond 0.04500 ( 286) hydrogen bonds : angle 4.55933 ( 861) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: U 103 MET cc_start: 0.8065 (ttt) cc_final: 0.7713 (ttt) REVERT: U 183 MET cc_start: 0.6768 (tpt) cc_final: 0.6013 (mtt) REVERT: U 339 ILE cc_start: 0.7647 (mm) cc_final: 0.7352 (mm) REVERT: S 153 ARG cc_start: 0.6820 (mtm-85) cc_final: 0.6211 (mtm-85) REVERT: S 515 ASP cc_start: 0.6857 (m-30) cc_final: 0.6069 (t0) REVERT: I 82 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6331 (pp) REVERT: I 155 ARG cc_start: 0.8787 (mtp85) cc_final: 0.8507 (mtt90) outliers start: 17 outliers final: 14 residues processed: 74 average time/residue: 0.0923 time to fit residues: 9.0120 Evaluate side-chains 73 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 52 HIS Chi-restraints excluded: chain U residue 161 VAL Chi-restraints excluded: chain U residue 169 THR Chi-restraints excluded: chain U residue 177 ILE Chi-restraints excluded: chain U residue 189 SER Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain U residue 303 GLU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 436 LYS Chi-restraints excluded: chain S residue 438 THR Chi-restraints excluded: chain S residue 462 LEU Chi-restraints excluded: chain S residue 561 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 120 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 61 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 3 optimal weight: 0.0570 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 301 GLN S 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.195806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.146363 restraints weight = 6842.059| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.37 r_work: 0.3653 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6769 Z= 0.126 Angle : 0.561 11.071 9159 Z= 0.281 Chirality : 0.040 0.166 1049 Planarity : 0.005 0.048 1154 Dihedral : 4.161 14.418 883 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.30 % Allowed : 12.72 % Favored : 84.98 % 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 are not related in a simple way. whole: -0.19 (0.30), residues: 803 helix: 1.16 (0.29), residues: 329 sheet: -0.09 (0.49), residues: 119 loop : -1.38 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 97 TYR 0.011 0.001 TYR U 168 PHE 0.011 0.001 PHE S 270 TRP 0.013 0.001 TRP S 554 HIS 0.004 0.001 HIS U 271 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6769) covalent geometry : angle 0.56081 ( 9159) hydrogen bonds : bond 0.04574 ( 286) hydrogen bonds : angle 4.56337 ( 861) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: U 103 MET cc_start: 0.8155 (ttt) cc_final: 0.7825 (ttt) REVERT: U 183 MET cc_start: 0.6859 (tpt) cc_final: 0.5998 (mtt) REVERT: U 339 ILE cc_start: 0.7727 (mm) cc_final: 0.7410 (mm) REVERT: S 153 ARG cc_start: 0.7003 (mtm-85) cc_final: 0.6420 (mtm-85) REVERT: S 459 MET cc_start: 0.6747 (mmp) cc_final: 0.6537 (mmt) REVERT: S 515 ASP cc_start: 0.6899 (m-30) cc_final: 0.6103 (t0) REVERT: I 82 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6326 (pp) outliers start: 17 outliers final: 15 residues processed: 76 average time/residue: 0.1008 time to fit residues: 9.9931 Evaluate side-chains 77 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 52 HIS Chi-restraints excluded: chain U residue 161 VAL Chi-restraints excluded: chain U residue 169 THR Chi-restraints excluded: chain U residue 177 ILE Chi-restraints excluded: chain U residue 189 SER Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain U residue 303 GLU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 436 LYS Chi-restraints excluded: chain S residue 438 THR Chi-restraints excluded: chain S residue 462 LEU Chi-restraints excluded: chain S residue 523 LYS Chi-restraints excluded: chain S residue 561 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 120 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 9 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 66 optimal weight: 0.0670 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 58 HIS U 301 GLN S 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.194410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.143909 restraints weight = 6862.072| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.46 r_work: 0.3631 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6769 Z= 0.135 Angle : 0.573 10.857 9159 Z= 0.288 Chirality : 0.040 0.170 1049 Planarity : 0.005 0.048 1154 Dihedral : 4.209 14.618 883 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.44 % Allowed : 12.86 % Favored : 84.71 % 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 are not related in a simple way. whole: -0.25 (0.30), residues: 803 helix: 1.12 (0.29), residues: 329 sheet: -0.12 (0.49), residues: 119 loop : -1.42 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 97 TYR 0.012 0.001 TYR U 168 PHE 0.011 0.001 PHE S 270 TRP 0.014 0.001 TRP S 554 HIS 0.005 0.001 HIS U 271 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6769) covalent geometry : angle 0.57350 ( 9159) hydrogen bonds : bond 0.04736 ( 286) hydrogen bonds : angle 4.60005 ( 861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2079.90 seconds wall clock time: 36 minutes 13.24 seconds (2173.24 seconds total)