Starting phenix.real_space_refine on Fri Aug 7 02:54:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30us_58070/08_2026/30us_58070.cif Found real_map, /net/cci-nas-00/data/ceres_data/30us_58070/08_2026/30us_58070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/30us_58070/08_2026/30us_58070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30us_58070/08_2026/30us_58070.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/30us_58070/08_2026/30us_58070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30us_58070/08_2026/30us_58070.map" } resolution = 3.0 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 40 5.16 5 C 5895 2.51 5 N 1534 2.21 5 O 1611 1.98 5 H 9113 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18193 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 7356 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 11, 'TRANS': 435} Chain breaks: 2 Chain: "B" Number of atoms: 7356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 7356 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 11, 'TRANS': 435} Chain breaks: 2 Chain: "C" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1802 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain breaks: 1 Chain: "D" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1679 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain breaks: 1 Time building chain proxies: 3.10, per 1000 atoms: 0.17 Number of scatterers: 18193 At special positions: 0 Unit cell: (116.848, 94.336, 122.208, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 O 1611 8.00 N 1534 7.00 C 5895 6.00 H 9113 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 407 " - pdb=" SG CYS C 481 " distance=2.03 Simple disulfide: pdb=" SG CYS D 407 " - pdb=" SG CYS D 481 " 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: 1.13 Conformation dependent library (CDL) restraints added in 481.3 milliseconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 9 sheets defined 52.1% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 3 through 37 removed outlier: 3.992A pdb=" N ASN A 7 " --> pdb=" O HIS A 3 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR A 27 " --> pdb=" O THR A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 45 through 70 removed outlier: 3.807A pdb=" N GLU A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLY A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 106 Processing helix chain 'A' and resid 110 through 139 removed outlier: 4.057A pdb=" N MET A 116 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 152 through 165 Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.643A pdb=" N LEU A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR A 203 " --> pdb=" O LYS A 199 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 204' Processing helix chain 'A' and resid 219 through 234 removed outlier: 4.072A pdb=" N ARG A 223 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASN A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 308 Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.981A pdb=" N ASN A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.085A pdb=" N GLU A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 4.234A pdb=" N TYR A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.717A pdb=" N VAL A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 452 removed outlier: 4.039A pdb=" N TYR A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 473 removed outlier: 3.514A pdb=" N ASP A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 37 removed outlier: 4.182A pdb=" N VAL B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 45 through 70 removed outlier: 3.775A pdb=" N GLU B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TRP B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 106 Processing helix chain 'B' and resid 110 through 140 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 152 through 165 Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'B' and resid 219 through 234 Processing helix chain 'B' and resid 273 through 308 Proline residue: B 297 - end of helix removed outlier: 3.564A pdb=" N LYS B 308 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 380 Processing helix chain 'B' and resid 385 through 392 removed outlier: 3.970A pdb=" N ASN B 389 " --> pdb=" O PRO B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.516A pdb=" N GLU B 409 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 removed outlier: 3.557A pdb=" N TYR B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.739A pdb=" N VAL B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 440 No H-bonds generated for 'chain 'B' and resid 438 through 440' Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 454 through 474 Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.586A pdb=" N ASP C 475 " --> pdb=" O LYS C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 497 removed outlier: 3.614A pdb=" N TYR C 495 " --> pdb=" O SER C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 501 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'D' and resid 447 through 450 Processing helix chain 'D' and resid 492 through 496 Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 196 removed outlier: 3.933A pdb=" N GLN A 193 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARG A 144 " --> pdb=" O ASN A 171 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 173 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR A 146 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE A 175 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE A 148 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP A 177 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 262 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 257 removed outlier: 3.556A pdb=" N VAL A 262 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE B 211 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP B 145 " --> pdb=" O GLN B 210 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE B 212 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TRP B 147 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ARG B 144 " --> pdb=" O ASN B 171 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 173 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THR B 146 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE B 175 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N GLN B 193 " --> pdb=" O ASN B 171 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL B 173 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ILE B 195 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE B 175 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AA4, first strand: chain 'A' and resid 319 through 320 Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 320 Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 6 removed outlier: 4.161A pdb=" N LEU C 405 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 444 through 445 removed outlier: 3.509A pdb=" N TYR C 444 " --> pdb=" O SER C 435 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N PHE C 432 " --> pdb=" O ARG C 423 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ARG C 423 " --> pdb=" O PHE C 432 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA C 434 " --> pdb=" O TRP C 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 418 through 419 Processing sheet with id=AA9, first strand: chain 'D' and resid 434 through 436 426 hydrogen bonds defined for protein. 1212 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: 3.79 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9105 1.03 - 1.23: 14 1.23 - 1.42: 4029 1.42 - 1.62: 5201 1.62 - 1.81: 68 Bond restraints: 18417 Sorted by residual: bond pdb=" N HIS B 3 " pdb=" CA HIS B 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N HIS A 3 " pdb=" CA HIS A 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N VAL D 2 " pdb=" CA VAL D 2 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.65e+00 bond pdb=" N VAL D 2 " pdb=" H VAL D 2 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" N HIS B 3 " pdb=" H HIS B 3 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 18412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 32882 1.81 - 3.61: 267 3.61 - 5.42: 29 5.42 - 7.22: 6 7.22 - 9.03: 1 Bond angle restraints: 33185 Sorted by residual: angle pdb=" CA LYS D 461 " pdb=" CB LYS D 461 " pdb=" CG LYS D 461 " ideal model delta sigma weight residual 114.10 120.54 -6.44 2.00e+00 2.50e-01 1.04e+01 angle pdb=" CG LYS A 305 " pdb=" CD LYS A 305 " pdb=" CE LYS A 305 " ideal model delta sigma weight residual 111.30 118.40 -7.10 2.30e+00 1.89e-01 9.54e+00 angle pdb=" CB MET A 254 " pdb=" CG MET A 254 " pdb=" SD MET A 254 " ideal model delta sigma weight residual 112.70 121.73 -9.03 3.00e+00 1.11e-01 9.05e+00 angle pdb=" CB LYS D 461 " pdb=" CG LYS D 461 " pdb=" CD LYS D 461 " ideal model delta sigma weight residual 111.30 118.02 -6.72 2.30e+00 1.89e-01 8.54e+00 angle pdb=" N VAL D 449 " pdb=" CA VAL D 449 " pdb=" C VAL D 449 " ideal model delta sigma weight residual 113.10 110.28 2.82 9.70e-01 1.06e+00 8.46e+00 ... (remaining 33180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 7694 17.82 - 35.65: 655 35.65 - 53.47: 217 53.47 - 71.29: 43 71.29 - 89.11: 13 Dihedral angle restraints: 8622 sinusoidal: 4587 harmonic: 4035 Sorted by residual: dihedral pdb=" CB CYS C 407 " pdb=" SG CYS C 407 " pdb=" SG CYS C 481 " pdb=" CB CYS C 481 " ideal model delta sinusoidal sigma weight residual 93.00 56.26 36.74 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" CA TYR B 315 " pdb=" C TYR B 315 " pdb=" N GLY B 316 " pdb=" CA GLY B 316 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PRO D 425 " pdb=" C PRO D 425 " pdb=" N PRO D 426 " pdb=" CA PRO D 426 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 8619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 881 0.028 - 0.057: 317 0.057 - 0.085: 115 0.085 - 0.114: 53 0.114 - 0.142: 23 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CA ILE A 369 " pdb=" N ILE A 369 " pdb=" C ILE A 369 " pdb=" CB ILE A 369 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ILE D 443 " pdb=" N ILE D 443 " pdb=" C ILE D 443 " pdb=" CB ILE D 443 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE A 212 " pdb=" N ILE A 212 " pdb=" C ILE A 212 " pdb=" CB ILE A 212 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 1386 not shown) Planarity restraints: 2635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 424 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO D 425 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 425 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 425 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 425 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO D 426 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 426 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 426 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 366 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO A 367 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 367 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 367 " -0.021 5.00e-02 4.00e+02 ... (remaining 2632 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.39: 7547 2.39 - 2.94: 41644 2.94 - 3.49: 47385 3.49 - 4.05: 61641 4.05 - 4.60: 91584 Nonbonded interactions: 249801 Sorted by model distance: nonbonded pdb=" HG2 ARG D 457 " pdb="HH11 ARG D 457 " model vdw 1.832 2.270 nonbonded pdb=" HE ARG B 72 " pdb=" HE1 TYR B 76 " model vdw 1.845 2.100 nonbonded pdb=" HZ PHE C 432 " pdb=" HG SER C 435 " model vdw 1.881 2.100 nonbonded pdb=" HG3 GLU A 50 " pdb=" H GLY A 51 " model vdw 1.903 2.270 nonbonded pdb=" HG3 ARG B 245 " pdb="HH11 ARG B 245 " model vdw 1.910 2.270 ... (remaining 249796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 2 through 403 or resid 406 through 507)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 16.190 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 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 0.038 9306 Z= 0.127 Angle : 0.563 9.025 12611 Z= 0.310 Chirality : 0.039 0.142 1389 Planarity : 0.004 0.053 1556 Dihedral : 15.086 89.113 3349 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 0.41 % Allowed : 17.90 % Favored : 81.69 % 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 are not related in a simple way. whole: 0.44 (0.26), residues: 1101 helix: 1.51 (0.25), residues: 464 sheet: -1.57 (0.40), residues: 176 loop : -0.07 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 457 TYR 0.022 0.001 TYR D 417 PHE 0.014 0.001 PHE A 40 TRP 0.010 0.001 TRP B 81 HIS 0.007 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 9304) covalent geometry : angle 0.56301 / 0.31 (12607) SS BOND : bond 0.00313 / 0.16 ( 2) SS BOND : angle 0.39754 / 0.26 ( 4) hydrogen bonds : bond 0.12296 / 7.94 ( 426) hydrogen bonds : angle 5.63106 / 4.16 ( 1212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 TYR cc_start: 0.8352 (m-80) cc_final: 0.8150 (m-10) REVERT: A 86 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7754 (mm-30) REVERT: A 254 MET cc_start: 0.7726 (tmm) cc_final: 0.7465 (tmm) REVERT: A 315 TYR cc_start: 0.8313 (t80) cc_final: 0.7596 (t80) REVERT: A 382 ASP cc_start: 0.8166 (m-30) cc_final: 0.7489 (t0) REVERT: A 411 TYR cc_start: 0.8378 (m-10) cc_final: 0.7975 (m-10) REVERT: B 86 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7305 (mt-10) REVERT: B 325 LYS cc_start: 0.9149 (ptpt) cc_final: 0.8910 (ptmm) REVERT: C 3 GLN cc_start: 0.8829 (pm20) cc_final: 0.8498 (mp10) REVERT: C 458 ASP cc_start: 0.8475 (t0) cc_final: 0.7852 (t0) REVERT: C 461 LYS cc_start: 0.9416 (pttp) cc_final: 0.9143 (pmtt) REVERT: C 467 GLN cc_start: 0.8825 (mm110) cc_final: 0.8144 (mm-40) REVERT: C 484 ASP cc_start: 0.7850 (t0) cc_final: 0.7510 (t0) outliers start: 4 outliers final: 3 residues processed: 97 average time/residue: 1.0268 time to fit residues: 108.0188 Evaluate side-chains 93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain C residue 469 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 424 GLN D 442 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.108433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.074561 restraints weight = 62548.627| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.45 r_work: 0.3210 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9306 Z= 0.197 Angle : 0.529 5.309 12611 Z= 0.286 Chirality : 0.040 0.139 1389 Planarity : 0.004 0.056 1556 Dihedral : 4.541 55.187 1245 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 2.03 % Allowed : 16.68 % 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 are not related in a simple way. whole: 0.78 (0.26), residues: 1101 helix: 1.88 (0.24), residues: 472 sheet: -1.38 (0.41), residues: 167 loop : -0.07 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 457 TYR 0.015 0.001 TYR D 417 PHE 0.013 0.001 PHE A 82 TRP 0.012 0.001 TRP B 81 HIS 0.005 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 ( 9304) covalent geometry : angle 0.52909 / 0.29 (12607) SS BOND : bond 0.00483 / 0.24 ( 2) SS BOND : angle 0.64198 / 0.40 ( 4) hydrogen bonds : bond 0.04343 / 2.89 ( 426) hydrogen bonds : angle 4.30478 / 3.17 ( 1212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 HIS cc_start: 0.7043 (OUTLIER) cc_final: 0.6467 (t-90) REVERT: A 86 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7949 (mm-30) REVERT: A 208 HIS cc_start: 0.6923 (p90) cc_final: 0.6587 (p-80) REVERT: A 269 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8466 (mm-40) REVERT: A 315 TYR cc_start: 0.8466 (t80) cc_final: 0.8019 (t80) REVERT: A 382 ASP cc_start: 0.8260 (m-30) cc_final: 0.7923 (t0) REVERT: A 411 TYR cc_start: 0.8321 (m-10) cc_final: 0.7994 (m-10) REVERT: B 254 MET cc_start: 0.8727 (ppp) cc_final: 0.8414 (ppp) REVERT: B 325 LYS cc_start: 0.9211 (ptpt) cc_final: 0.8970 (ptmm) REVERT: B 372 ILE cc_start: 0.9229 (mm) cc_final: 0.9029 (tp) REVERT: C 3 GLN cc_start: 0.8846 (pm20) cc_final: 0.8426 (mp10) REVERT: C 419 MET cc_start: 0.7654 (mmp) cc_final: 0.7437 (mmp) REVERT: C 467 GLN cc_start: 0.8779 (mm110) cc_final: 0.8095 (mp10) REVERT: C 484 ASP cc_start: 0.8332 (t0) cc_final: 0.7838 (t0) REVERT: D 412 ARG cc_start: 0.7680 (ptt-90) cc_final: 0.7085 (ptt-90) outliers start: 20 outliers final: 10 residues processed: 109 average time/residue: 0.8312 time to fit residues: 99.2945 Evaluate side-chains 95 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 458 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.108167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.073808 restraints weight = 62499.396| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.48 r_work: 0.3223 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9306 Z= 0.159 Angle : 0.502 5.153 12611 Z= 0.270 Chirality : 0.039 0.139 1389 Planarity : 0.004 0.054 1556 Dihedral : 4.430 56.000 1243 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 1.42 % Allowed : 16.99 % Favored : 81.59 % 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: 0.88 (0.26), residues: 1101 helix: 2.06 (0.23), residues: 486 sheet: -1.38 (0.41), residues: 167 loop : -0.19 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 457 TYR 0.009 0.001 TYR D 495 PHE 0.011 0.001 PHE A 94 TRP 0.009 0.001 TRP B 52 HIS 0.005 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 9304) covalent geometry : angle 0.50194 / 0.27 (12607) SS BOND : bond 0.00411 / 0.21 ( 2) SS BOND : angle 0.55823 / 0.34 ( 4) hydrogen bonds : bond 0.04176 / 2.78 ( 426) hydrogen bonds : angle 4.11962 / 3.05 ( 1212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7876 (mm-30) REVERT: A 269 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8398 (mm-40) REVERT: A 315 TYR cc_start: 0.8423 (t80) cc_final: 0.7738 (t80) REVERT: A 382 ASP cc_start: 0.8315 (m-30) cc_final: 0.7912 (t0) REVERT: A 411 TYR cc_start: 0.8355 (m-10) cc_final: 0.8017 (m-10) REVERT: B 254 MET cc_start: 0.8726 (ppp) cc_final: 0.8395 (ppp) REVERT: B 325 LYS cc_start: 0.9225 (ptpt) cc_final: 0.8978 (ptmm) REVERT: B 372 ILE cc_start: 0.9194 (mm) cc_final: 0.8983 (tp) REVERT: C 3 GLN cc_start: 0.8864 (pm20) cc_final: 0.8479 (mp10) REVERT: C 467 GLN cc_start: 0.8773 (mm110) cc_final: 0.8277 (mp10) REVERT: C 468 MET cc_start: 0.8186 (tpt) cc_final: 0.7969 (tpp) REVERT: C 484 ASP cc_start: 0.8269 (t0) cc_final: 0.7756 (t0) REVERT: D 412 ARG cc_start: 0.7627 (ptt-90) cc_final: 0.6972 (ptt-90) outliers start: 14 outliers final: 8 residues processed: 102 average time/residue: 1.0135 time to fit residues: 112.7445 Evaluate side-chains 91 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 469 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.107832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.073483 restraints weight = 62750.716| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.52 r_work: 0.3208 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9306 Z= 0.146 Angle : 0.493 5.242 12611 Z= 0.264 Chirality : 0.039 0.137 1389 Planarity : 0.004 0.054 1556 Dihedral : 4.092 18.843 1241 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 1.42 % Allowed : 17.29 % 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 are not related in a simple way. whole: 1.02 (0.27), residues: 1101 helix: 2.22 (0.24), residues: 484 sheet: -1.36 (0.42), residues: 167 loop : -0.15 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 77 TYR 0.014 0.001 TYR D 417 PHE 0.013 0.001 PHE B 40 TRP 0.009 0.001 TRP B 456 HIS 0.004 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 9304) covalent geometry : angle 0.49340 / 0.26 (12607) SS BOND : bond 0.00399 / 0.20 ( 2) SS BOND : angle 0.56225 / 0.33 ( 4) hydrogen bonds : bond 0.03929 / 2.62 ( 426) hydrogen bonds : angle 3.99672 / 2.96 ( 1212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7980 (mm-30) REVERT: A 208 HIS cc_start: 0.6873 (p90) cc_final: 0.6499 (p-80) REVERT: A 315 TYR cc_start: 0.8481 (t80) cc_final: 0.7790 (t80) REVERT: A 382 ASP cc_start: 0.8362 (m-30) cc_final: 0.7902 (t0) REVERT: A 411 TYR cc_start: 0.8339 (m-10) cc_final: 0.7850 (m-10) REVERT: B 254 MET cc_start: 0.8788 (ppp) cc_final: 0.8534 (ppp) REVERT: B 325 LYS cc_start: 0.9236 (ptpt) cc_final: 0.8994 (ptmm) REVERT: B 372 ILE cc_start: 0.9196 (mm) cc_final: 0.8994 (tp) REVERT: C 3 GLN cc_start: 0.8852 (pm20) cc_final: 0.8470 (mp10) REVERT: C 419 MET cc_start: 0.7622 (mmp) cc_final: 0.7123 (mmp) REVERT: C 467 GLN cc_start: 0.8821 (mm110) cc_final: 0.8306 (mp10) REVERT: C 468 MET cc_start: 0.8243 (tpt) cc_final: 0.8023 (tpp) REVERT: C 484 ASP cc_start: 0.8287 (t0) cc_final: 0.7735 (t0) REVERT: D 412 ARG cc_start: 0.7608 (ptt-90) cc_final: 0.6775 (ppt170) outliers start: 14 outliers final: 8 residues processed: 99 average time/residue: 1.0263 time to fit residues: 110.8423 Evaluate side-chains 91 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 469 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.106856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.072348 restraints weight = 62923.136| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.49 r_work: 0.3132 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9306 Z= 0.184 Angle : 0.510 5.183 12611 Z= 0.275 Chirality : 0.040 0.135 1389 Planarity : 0.004 0.054 1556 Dihedral : 4.126 18.650 1241 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.73 % Rotamer: Outliers : 2.34 % Allowed : 16.68 % Favored : 80.98 % 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: 0.90 (0.27), residues: 1101 helix: 2.11 (0.24), residues: 488 sheet: -1.32 (0.42), residues: 167 loop : -0.25 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 245 TYR 0.014 0.001 TYR D 501 PHE 0.017 0.001 PHE B 40 TRP 0.010 0.001 TRP B 456 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 9304) covalent geometry : angle 0.51033 / 0.28 (12607) SS BOND : bond 0.00454 / 0.23 ( 2) SS BOND : angle 0.62138 / 0.38 ( 4) hydrogen bonds : bond 0.04046 / 2.70 ( 426) hydrogen bonds : angle 4.01097 / 2.96 ( 1212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.8521 (t80) cc_final: 0.7871 (t80) REVERT: A 382 ASP cc_start: 0.8458 (m-30) cc_final: 0.8060 (t0) REVERT: A 411 TYR cc_start: 0.8315 (m-10) cc_final: 0.7960 (m-10) REVERT: B 143 MET cc_start: 0.8752 (mmt) cc_final: 0.8372 (mmm) REVERT: B 254 MET cc_start: 0.8827 (ppp) cc_final: 0.8549 (ppp) REVERT: B 269 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8584 (mm-40) REVERT: B 325 LYS cc_start: 0.9244 (ptpt) cc_final: 0.9003 (ptmm) REVERT: B 372 ILE cc_start: 0.9196 (mm) cc_final: 0.8991 (tp) REVERT: B 411 TYR cc_start: 0.8229 (m-10) cc_final: 0.7810 (m-10) REVERT: C 3 GLN cc_start: 0.8845 (pm20) cc_final: 0.8486 (mp10) REVERT: C 419 MET cc_start: 0.7724 (mmp) cc_final: 0.7254 (mmp) REVERT: C 467 GLN cc_start: 0.8856 (mm110) cc_final: 0.8300 (mp10) REVERT: C 468 MET cc_start: 0.8354 (tpt) cc_final: 0.8124 (tpp) REVERT: C 484 ASP cc_start: 0.8349 (t0) cc_final: 0.7913 (t0) REVERT: D 412 ARG cc_start: 0.7492 (ptt-90) cc_final: 0.6748 (ptt-90) outliers start: 23 outliers final: 10 residues processed: 104 average time/residue: 1.0111 time to fit residues: 114.6851 Evaluate side-chains 95 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain C residue 469 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.106483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.072609 restraints weight = 62412.781| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.37 r_work: 0.3027 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9306 Z= 0.109 Angle : 0.489 5.358 12611 Z= 0.258 Chirality : 0.039 0.135 1389 Planarity : 0.004 0.054 1556 Dihedral : 4.007 18.625 1240 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 1.63 % Allowed : 17.90 % Favored : 80.47 % 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: 1.13 (0.27), residues: 1101 helix: 2.34 (0.24), residues: 486 sheet: -1.23 (0.43), residues: 167 loop : -0.17 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.016 0.001 TYR D 417 PHE 0.019 0.001 PHE B 40 TRP 0.008 0.001 TRP B 456 HIS 0.004 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 9304) covalent geometry : angle 0.48873 / 0.26 (12607) SS BOND : bond 0.00356 / 0.18 ( 2) SS BOND : angle 0.52196 / 0.30 ( 4) hydrogen bonds : bond 0.03622 / 2.41 ( 426) hydrogen bonds : angle 3.78469 / 2.79 ( 1212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.8575 (t80) cc_final: 0.7930 (t80) REVERT: A 335 MET cc_start: 0.6467 (mpp) cc_final: 0.6018 (mmm) REVERT: A 382 ASP cc_start: 0.8491 (m-30) cc_final: 0.8137 (t0) REVERT: A 411 TYR cc_start: 0.8215 (m-10) cc_final: 0.7870 (m-10) REVERT: B 143 MET cc_start: 0.8912 (mmt) cc_final: 0.8554 (mmm) REVERT: B 254 MET cc_start: 0.8941 (ppp) cc_final: 0.8687 (ppp) REVERT: B 269 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8693 (mm-40) REVERT: B 325 LYS cc_start: 0.9304 (ptpt) cc_final: 0.9086 (ptmm) REVERT: B 372 ILE cc_start: 0.9212 (mm) cc_final: 0.8991 (tp) REVERT: C 3 GLN cc_start: 0.8713 (pm20) cc_final: 0.8342 (mp10) REVERT: C 467 GLN cc_start: 0.8789 (mm110) cc_final: 0.8219 (mp10) REVERT: C 468 MET cc_start: 0.8259 (tpt) cc_final: 0.8038 (tpp) REVERT: C 484 ASP cc_start: 0.8402 (t0) cc_final: 0.7958 (t0) REVERT: D 412 ARG cc_start: 0.7408 (ptt-90) cc_final: 0.6638 (ptt-90) outliers start: 16 outliers final: 7 residues processed: 101 average time/residue: 1.0581 time to fit residues: 115.6958 Evaluate side-chains 93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 469 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.105447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.071365 restraints weight = 63260.689| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.38 r_work: 0.2987 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9306 Z= 0.166 Angle : 0.513 5.993 12611 Z= 0.272 Chirality : 0.039 0.136 1389 Planarity : 0.004 0.054 1556 Dihedral : 4.010 18.421 1240 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 1.42 % Allowed : 18.21 % Favored : 80.37 % 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: 1.04 (0.27), residues: 1101 helix: 2.26 (0.24), residues: 488 sheet: -1.27 (0.43), residues: 167 loop : -0.22 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 368 TYR 0.014 0.001 TYR D 501 PHE 0.019 0.001 PHE B 40 TRP 0.010 0.001 TRP B 456 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 9304) covalent geometry : angle 0.51300 / 0.27 (12607) SS BOND : bond 0.00396 / 0.20 ( 2) SS BOND : angle 0.57667 / 0.35 ( 4) hydrogen bonds : bond 0.03788 / 2.52 ( 426) hydrogen bonds : angle 3.86332 / 2.84 ( 1212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.8571 (t80) cc_final: 0.7941 (t80) REVERT: A 411 TYR cc_start: 0.8227 (m-10) cc_final: 0.7797 (m-10) REVERT: B 143 MET cc_start: 0.8919 (mmt) cc_final: 0.8558 (mmm) REVERT: B 254 MET cc_start: 0.8998 (ppp) cc_final: 0.8741 (ppp) REVERT: B 269 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8706 (mm-40) REVERT: B 325 LYS cc_start: 0.9283 (ptpt) cc_final: 0.9042 (ptmm) REVERT: B 372 ILE cc_start: 0.9212 (mm) cc_final: 0.8990 (tp) REVERT: C 3 GLN cc_start: 0.8722 (pm20) cc_final: 0.8355 (mp10) REVERT: C 467 GLN cc_start: 0.8797 (mm110) cc_final: 0.8288 (mp10) REVERT: C 484 ASP cc_start: 0.8400 (t0) cc_final: 0.7960 (t0) outliers start: 14 outliers final: 8 residues processed: 94 average time/residue: 0.9875 time to fit residues: 100.7230 Evaluate side-chains 91 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 469 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.104428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.070296 restraints weight = 63615.284| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.37 r_work: 0.2964 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 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 : 0.005 0.040 9306 Z= 0.200 Angle : 0.540 9.049 12611 Z= 0.288 Chirality : 0.040 0.138 1389 Planarity : 0.004 0.055 1556 Dihedral : 4.098 18.507 1240 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 2.24 % Allowed : 17.90 % Favored : 79.86 % 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: 0.90 (0.27), residues: 1101 helix: 2.12 (0.23), residues: 488 sheet: -1.37 (0.42), residues: 167 loop : -0.26 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 245 TYR 0.020 0.001 TYR D 417 PHE 0.026 0.002 PHE B 40 TRP 0.011 0.001 TRP B 456 HIS 0.005 0.001 HIS B 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 9304) covalent geometry : angle 0.53997 / 0.29 (12607) SS BOND : bond 0.00412 / 0.21 ( 2) SS BOND : angle 0.69977 / 0.44 ( 4) hydrogen bonds : bond 0.04044 / 2.70 ( 426) hydrogen bonds : angle 3.95115 / 2.90 ( 1212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.8563 (t80) cc_final: 0.7897 (t80) REVERT: A 382 ASP cc_start: 0.8208 (m-30) cc_final: 0.7710 (p0) REVERT: A 411 TYR cc_start: 0.8249 (m-10) cc_final: 0.7818 (m-10) REVERT: B 254 MET cc_start: 0.9016 (ppp) cc_final: 0.8754 (ppp) REVERT: B 325 LYS cc_start: 0.9292 (ptpt) cc_final: 0.9048 (ptmm) REVERT: B 372 ILE cc_start: 0.9228 (mm) cc_final: 0.9001 (tp) REVERT: C 3 GLN cc_start: 0.8712 (pm20) cc_final: 0.8365 (mp10) REVERT: C 419 MET cc_start: 0.7776 (mmp) cc_final: 0.7340 (mmp) REVERT: C 467 GLN cc_start: 0.8961 (mm110) cc_final: 0.8222 (mp10) REVERT: C 468 MET cc_start: 0.7892 (tpp) cc_final: 0.7602 (tpp) REVERT: C 484 ASP cc_start: 0.8428 (t0) cc_final: 0.7943 (t0) outliers start: 22 outliers final: 10 residues processed: 98 average time/residue: 1.0023 time to fit residues: 106.8207 Evaluate side-chains 91 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 469 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 101 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.106165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.072209 restraints weight = 62976.862| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.38 r_work: 0.3007 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9306 Z= 0.106 Angle : 0.509 7.353 12611 Z= 0.264 Chirality : 0.039 0.140 1389 Planarity : 0.004 0.090 1556 Dihedral : 4.000 18.326 1240 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 0.92 % Allowed : 19.43 % 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 are not related in a simple way. whole: 1.09 (0.27), residues: 1101 helix: 2.32 (0.24), residues: 488 sheet: -1.31 (0.42), residues: 167 loop : -0.20 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 245 TYR 0.009 0.001 TYR D 501 PHE 0.025 0.001 PHE B 40 TRP 0.009 0.001 TRP B 118 HIS 0.004 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9304) covalent geometry : angle 0.50939 / 0.26 (12607) SS BOND : bond 0.00321 / 0.17 ( 2) SS BOND : angle 0.50267 / 0.32 ( 4) hydrogen bonds : bond 0.03534 / 2.35 ( 426) hydrogen bonds : angle 3.72775 / 2.74 ( 1212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8465 (mm-40) REVERT: A 315 TYR cc_start: 0.8544 (t80) cc_final: 0.7860 (t80) REVERT: A 382 ASP cc_start: 0.8192 (m-30) cc_final: 0.7675 (OUTLIER) REVERT: A 411 TYR cc_start: 0.8237 (m-10) cc_final: 0.7783 (m-10) REVERT: B 254 MET cc_start: 0.9005 (ppp) cc_final: 0.8731 (ppp) REVERT: B 325 LYS cc_start: 0.9285 (ptpt) cc_final: 0.9059 (ptmm) REVERT: B 372 ILE cc_start: 0.9227 (mm) cc_final: 0.9002 (tp) REVERT: C 3 GLN cc_start: 0.8702 (pm20) cc_final: 0.8350 (mp10) REVERT: C 467 GLN cc_start: 0.8897 (mm110) cc_final: 0.8207 (mp10) REVERT: C 468 MET cc_start: 0.7698 (tpp) cc_final: 0.7335 (tpp) REVERT: C 484 ASP cc_start: 0.8438 (t0) cc_final: 0.7999 (t0) REVERT: D 447 ASP cc_start: 0.8055 (m-30) cc_final: 0.7639 (OUTLIER) outliers start: 9 outliers final: 7 residues processed: 92 average time/residue: 1.0071 time to fit residues: 100.9609 Evaluate side-chains 87 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 469 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.105744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.071724 restraints weight = 63281.143| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.39 r_work: 0.2995 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9306 Z= 0.131 Angle : 0.522 7.021 12611 Z= 0.274 Chirality : 0.039 0.140 1389 Planarity : 0.004 0.098 1556 Dihedral : 3.968 18.175 1240 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 0.71 % Allowed : 19.74 % Favored : 79.55 % 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: 1.08 (0.27), residues: 1101 helix: 2.27 (0.24), residues: 490 sheet: -1.33 (0.42), residues: 167 loop : -0.13 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 245 TYR 0.021 0.001 TYR D 417 PHE 0.031 0.001 PHE B 40 TRP 0.009 0.001 TRP B 456 HIS 0.004 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 9304) covalent geometry : angle 0.52198 / 0.27 (12607) SS BOND : bond 0.00356 / 0.18 ( 2) SS BOND : angle 0.53795 / 0.34 ( 4) hydrogen bonds : bond 0.03565 / 2.37 ( 426) hydrogen bonds : angle 3.75085 / 2.75 ( 1212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.8569 (t80) cc_final: 0.7974 (t80) REVERT: A 382 ASP cc_start: 0.8201 (m-30) cc_final: 0.7667 (p0) REVERT: A 411 TYR cc_start: 0.8214 (m-10) cc_final: 0.7773 (m-10) REVERT: B 254 MET cc_start: 0.8959 (ppp) cc_final: 0.8688 (ppp) REVERT: B 325 LYS cc_start: 0.9265 (ptpt) cc_final: 0.9034 (ptmm) REVERT: B 372 ILE cc_start: 0.9222 (mm) cc_final: 0.8993 (tp) REVERT: C 3 GLN cc_start: 0.8676 (pm20) cc_final: 0.8338 (mp10) REVERT: C 419 MET cc_start: 0.7812 (mmp) cc_final: 0.7289 (mmp) REVERT: C 467 GLN cc_start: 0.8893 (mm110) cc_final: 0.8223 (mp10) REVERT: C 468 MET cc_start: 0.7880 (tpp) cc_final: 0.7568 (tpp) REVERT: C 484 ASP cc_start: 0.8439 (t0) cc_final: 0.7972 (t0) outliers start: 7 outliers final: 7 residues processed: 91 average time/residue: 1.0509 time to fit residues: 104.2224 Evaluate side-chains 90 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 469 ASN Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 471 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.106225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.072304 restraints weight = 63234.401| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.39 r_work: 0.2995 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9306 Z= 0.121 Angle : 0.518 7.453 12611 Z= 0.269 Chirality : 0.039 0.142 1389 Planarity : 0.004 0.087 1556 Dihedral : 3.939 18.241 1240 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 0.92 % Allowed : 19.53 % Favored : 79.55 % 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: 1.12 (0.27), residues: 1101 helix: 2.29 (0.24), residues: 490 sheet: -1.27 (0.42), residues: 167 loop : -0.14 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 245 TYR 0.011 0.001 TYR D 501 PHE 0.031 0.001 PHE B 40 TRP 0.008 0.001 TRP B 456 HIS 0.004 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9304) covalent geometry : angle 0.51792 / 0.27 (12607) SS BOND : bond 0.00348 / 0.18 ( 2) SS BOND : angle 0.53058 / 0.34 ( 4) hydrogen bonds : bond 0.03479 / 2.31 ( 426) hydrogen bonds : angle 3.71529 / 2.73 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4711.39 seconds wall clock time: 80 minutes 34.18 seconds (4834.18 seconds total)