Starting phenix.real_space_refine on Fri Aug 22 20:27:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzs_36752/08_2025/8jzs_36752.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzs_36752/08_2025/8jzs_36752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jzs_36752/08_2025/8jzs_36752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzs_36752/08_2025/8jzs_36752.map" model { file = "/net/cci-nas-00/data/ceres_data/8jzs_36752/08_2025/8jzs_36752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzs_36752/08_2025/8jzs_36752.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.092 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 40 5.16 5 C 4996 2.51 5 N 1190 2.21 5 O 1274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7500 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3680 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 464} Chain breaks: 4 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3680 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 464} Chain breaks: 4 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'CLR': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'CLR': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.97, per 1000 atoms: 0.26 Number of scatterers: 7500 At special positions: 0 Unit cell: (119.671, 88.9299, 91.1257, 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 40 16.00 O 1274 8.00 N 1190 7.00 C 4996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 436 " " NAG B 601 " - " ASN B 436 " Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 335.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 78.3% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 18 through 28 Processing helix chain 'B' and resid 34 through 57 removed outlier: 3.502A pdb=" N GLY B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 70 through 98 removed outlier: 4.255A pdb=" N SER B 89 " --> pdb=" O THR B 85 " (cutoff:3.500A) Proline residue: B 90 - end of helix Processing helix chain 'B' and resid 101 through 118 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.866A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 removed outlier: 4.452A pdb=" N ALA B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 184 removed outlier: 3.503A pdb=" N ASN B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix removed outlier: 4.035A pdb=" N GLN B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 212 removed outlier: 3.572A pdb=" N ASN B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 removed outlier: 3.631A pdb=" N GLN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 243 removed outlier: 3.502A pdb=" N ILE B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) Proline residue: B 229 - end of helix removed outlier: 3.847A pdb=" N PHE B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 310 through 327 removed outlier: 3.756A pdb=" N ASP B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Proline residue: B 323 - end of helix Processing helix chain 'B' and resid 328 through 348 removed outlier: 3.828A pdb=" N VAL B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 389 removed outlier: 4.133A pdb=" N THR B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 372 " --> pdb=" O TRP B 368 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 374 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Proline residue: B 382 - end of helix Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.866A pdb=" N HIS B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.951A pdb=" N LYS B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 479 removed outlier: 3.590A pdb=" N TYR B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER B 469 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 510 Processing helix chain 'B' and resid 531 through 558 removed outlier: 3.544A pdb=" N TYR B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 28 Processing helix chain 'A' and resid 34 through 57 removed outlier: 3.503A pdb=" N GLY A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 70 through 98 removed outlier: 4.255A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 101 through 118 Processing helix chain 'A' and resid 118 through 125 removed outlier: 3.866A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 removed outlier: 4.452A pdb=" N ALA A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 184 removed outlier: 3.503A pdb=" N ASN A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 4.035A pdb=" N GLN A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 212 removed outlier: 3.572A pdb=" N ASN A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 removed outlier: 3.631A pdb=" N GLN A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 243 removed outlier: 3.502A pdb=" N ILE A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 3.847A pdb=" N PHE A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 310 through 327 removed outlier: 3.756A pdb=" N ASP A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 328 through 348 removed outlier: 3.828A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 389 removed outlier: 4.133A pdb=" N THR A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 372 " --> pdb=" O TRP A 368 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Proline residue: A 382 - end of helix Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.865A pdb=" N HIS A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 431 removed outlier: 3.951A pdb=" N LYS A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 479 removed outlier: 3.590A pdb=" N TYR A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 473 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 510 Processing helix chain 'A' and resid 531 through 558 removed outlier: 3.544A pdb=" N TYR A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 349 through 350 removed outlier: 3.655A pdb=" N VAL B 442 " --> pdb=" O ILE B 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 349 through 350 removed outlier: 3.655A pdb=" N VAL A 442 " --> pdb=" O ILE A 439 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1551 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: 1.37 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1126 1.30 - 1.43: 2046 1.43 - 1.55: 4456 1.55 - 1.68: 2 1.68 - 1.81: 62 Bond restraints: 7692 Sorted by residual: bond pdb=" CA ALA B 35 " pdb=" C ALA B 35 " ideal model delta sigma weight residual 1.524 1.438 0.085 1.32e-02 5.74e+03 4.19e+01 bond pdb=" CA ALA A 35 " pdb=" C ALA A 35 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.32e-02 5.74e+03 4.13e+01 bond pdb=" CA GLU A 189 " pdb=" C GLU A 189 " ideal model delta sigma weight residual 1.520 1.439 0.081 1.39e-02 5.18e+03 3.37e+01 bond pdb=" CA GLU B 189 " pdb=" C GLU B 189 " ideal model delta sigma weight residual 1.520 1.440 0.080 1.39e-02 5.18e+03 3.31e+01 bond pdb=" CA PRO A 188 " pdb=" CB PRO A 188 " ideal model delta sigma weight residual 1.533 1.452 0.081 1.42e-02 4.96e+03 3.28e+01 ... (remaining 7687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 10081 2.06 - 4.12: 276 4.12 - 6.19: 93 6.19 - 8.25: 22 8.25 - 10.31: 12 Bond angle restraints: 10484 Sorted by residual: angle pdb=" N GLU A 189 " pdb=" CA GLU A 189 " pdb=" C GLU A 189 " ideal model delta sigma weight residual 114.31 104.00 10.31 1.29e+00 6.01e-01 6.39e+01 angle pdb=" N GLU B 189 " pdb=" CA GLU B 189 " pdb=" C GLU B 189 " ideal model delta sigma weight residual 114.31 104.02 10.29 1.29e+00 6.01e-01 6.36e+01 angle pdb=" C GLY B 28 " pdb=" N ALA B 29 " pdb=" CA ALA B 29 " ideal model delta sigma weight residual 121.86 131.16 -9.30 1.65e+00 3.67e-01 3.17e+01 angle pdb=" C GLY A 28 " pdb=" N ALA A 29 " pdb=" CA ALA A 29 " ideal model delta sigma weight residual 121.86 131.13 -9.27 1.65e+00 3.67e-01 3.16e+01 angle pdb=" C PRO B 188 " pdb=" CA PRO B 188 " pdb=" CB PRO B 188 " ideal model delta sigma weight residual 111.56 102.73 8.83 1.65e+00 3.67e-01 2.86e+01 ... (remaining 10479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 4073 14.98 - 29.96: 453 29.96 - 44.93: 102 44.93 - 59.91: 30 59.91 - 74.89: 4 Dihedral angle restraints: 4662 sinusoidal: 1892 harmonic: 2770 Sorted by residual: dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 153 " pdb=" CB CYS B 153 " ideal model delta sinusoidal sigma weight residual 93.00 57.08 35.92 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 153 " pdb=" CB CYS A 153 " ideal model delta sinusoidal sigma weight residual 93.00 57.08 35.92 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CA PRO A 390 " pdb=" C PRO A 390 " pdb=" N ILE A 391 " pdb=" CA ILE A 391 " ideal model delta harmonic sigma weight residual -180.00 -159.71 -20.29 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1129 0.082 - 0.163: 83 0.163 - 0.245: 18 0.245 - 0.327: 10 0.327 - 0.408: 4 Chirality restraints: 1244 Sorted by residual: chirality pdb=" C13 CLR B 603 " pdb=" C12 CLR B 603 " pdb=" C14 CLR B 603 " pdb=" C17 CLR B 603 " both_signs ideal model delta sigma weight residual False -2.93 -2.52 -0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" C13 CLR A 602 " pdb=" C12 CLR A 602 " pdb=" C14 CLR A 602 " pdb=" C17 CLR A 602 " both_signs ideal model delta sigma weight residual False -2.93 -2.53 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C14 CLR A 602 " pdb=" C13 CLR A 602 " pdb=" C15 CLR A 602 " pdb=" C8 CLR A 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 1241 not shown) Planarity restraints: 1268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 389 " 0.051 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO B 390 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 390 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 390 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 389 " 0.051 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO A 390 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 390 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 390 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 187 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C GLY A 187 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY A 187 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO A 188 " 0.015 2.00e-02 2.50e+03 ... (remaining 1265 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2245 2.82 - 3.34: 7525 3.34 - 3.86: 12346 3.86 - 4.38: 14366 4.38 - 4.90: 24720 Nonbonded interactions: 61202 Sorted by model distance: nonbonded pdb=" C21 CLR B 602 " pdb=" C23 CLR B 602 " model vdw 2.299 3.088 nonbonded pdb=" C21 CLR A 603 " pdb=" C23 CLR A 603 " model vdw 2.300 3.088 nonbonded pdb=" OE2 GLU A 309 " pdb=" NZ LYS A 311 " model vdw 2.364 3.120 nonbonded pdb=" OE2 GLU B 309 " pdb=" NZ LYS B 311 " model vdw 2.364 3.120 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG SER A 255 " model vdw 2.373 3.040 ... (remaining 61197 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.590 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 0.008 0.085 7696 Z= 0.498 Angle : 0.959 14.925 10494 Z= 0.511 Chirality : 0.059 0.408 1244 Planarity : 0.006 0.078 1266 Dihedral : 13.269 74.890 2880 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.41 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.29), residues: 952 helix: 1.17 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.50 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.015 0.001 TYR B 335 PHE 0.021 0.001 PHE A 237 TRP 0.007 0.001 TRP B 452 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00754 ( 7692) covalent geometry : angle 0.93070 (10484) SS BOND : bond 0.00292 ( 2) SS BOND : angle 0.40998 ( 4) hydrogen bonds : bond 0.16320 ( 519) hydrogen bonds : angle 6.48046 ( 1551) link_NAG-ASN : bond 0.00249 ( 2) link_NAG-ASN : angle 9.73488 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 MET cc_start: 0.8525 (ttp) cc_final: 0.8273 (ttp) REVERT: A 413 MET cc_start: 0.8506 (ttp) cc_final: 0.8245 (ttp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.3620 time to fit residues: 58.7202 Evaluate side-chains 90 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.0570 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.0570 chunk 74 optimal weight: 0.8980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN B 63 ASN B 196 ASN B 457 GLN A 57 ASN A 63 ASN A 196 ASN A 457 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.143331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.110314 restraints weight = 9485.164| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.78 r_work: 0.3125 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7696 Z= 0.141 Angle : 0.625 8.252 10494 Z= 0.308 Chirality : 0.039 0.154 1244 Planarity : 0.005 0.058 1266 Dihedral : 8.038 53.830 1328 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.15 % Favored : 96.64 % Rotamer: Outliers : 1.60 % Allowed : 9.44 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.28), residues: 952 helix: 1.64 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -1.91 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 33 TYR 0.007 0.001 TYR B 458 PHE 0.018 0.001 PHE A 240 TRP 0.011 0.001 TRP A 453 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7692) covalent geometry : angle 0.62119 (10484) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.33992 ( 4) hydrogen bonds : bond 0.04564 ( 519) hydrogen bonds : angle 4.43245 ( 1551) link_NAG-ASN : bond 0.00045 ( 2) link_NAG-ASN : angle 2.89555 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 THR cc_start: 0.8935 (m) cc_final: 0.8668 (m) REVERT: B 413 MET cc_start: 0.9086 (ttp) cc_final: 0.8724 (ttp) REVERT: A 222 PHE cc_start: 0.8375 (m-80) cc_final: 0.8151 (m-80) REVERT: A 340 THR cc_start: 0.8930 (m) cc_final: 0.8666 (m) REVERT: A 413 MET cc_start: 0.9067 (ttp) cc_final: 0.8688 (ttp) outliers start: 12 outliers final: 2 residues processed: 105 average time/residue: 0.3544 time to fit residues: 40.1953 Evaluate side-chains 94 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain A residue 84 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN A 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.095651 restraints weight = 9390.467| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.76 r_work: 0.2911 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 7696 Z= 0.197 Angle : 0.666 7.292 10494 Z= 0.331 Chirality : 0.042 0.222 1244 Planarity : 0.005 0.055 1266 Dihedral : 7.388 49.498 1328 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.10 % Favored : 95.69 % Rotamer: Outliers : 3.99 % Allowed : 11.30 % 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 aren not related in a simple way. whole: 1.42 (0.28), residues: 952 helix: 1.79 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -1.62 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 393 TYR 0.025 0.002 TYR A 113 PHE 0.014 0.002 PHE B 194 TRP 0.010 0.002 TRP B 197 HIS 0.003 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 7692) covalent geometry : angle 0.66478 (10484) SS BOND : bond 0.00135 ( 2) SS BOND : angle 0.30756 ( 4) hydrogen bonds : bond 0.05737 ( 519) hydrogen bonds : angle 4.44705 ( 1551) link_NAG-ASN : bond 0.00160 ( 2) link_NAG-ASN : angle 1.58153 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.8630 (mmm) cc_final: 0.8303 (tpt) REVERT: B 320 LYS cc_start: 0.7819 (tttt) cc_final: 0.7509 (mtpm) REVERT: B 340 THR cc_start: 0.8904 (m) cc_final: 0.8636 (m) REVERT: B 413 MET cc_start: 0.9085 (ttp) cc_final: 0.8697 (ttp) REVERT: B 513 LYS cc_start: 0.7460 (pmtt) cc_final: 0.7243 (pmmt) REVERT: A 320 LYS cc_start: 0.7732 (tttt) cc_final: 0.7429 (mtpm) REVERT: A 340 THR cc_start: 0.8905 (m) cc_final: 0.8630 (m) REVERT: A 413 MET cc_start: 0.9069 (ttp) cc_final: 0.8669 (ttp) REVERT: A 513 LYS cc_start: 0.7461 (pmtt) cc_final: 0.7245 (pmmt) outliers start: 30 outliers final: 13 residues processed: 110 average time/residue: 0.3701 time to fit residues: 44.2704 Evaluate side-chains 94 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 92 optimal weight: 0.4980 chunk 48 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN A 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103591 restraints weight = 9417.822| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.63 r_work: 0.3144 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7696 Z= 0.140 Angle : 0.596 7.767 10494 Z= 0.293 Chirality : 0.040 0.198 1244 Planarity : 0.004 0.035 1266 Dihedral : 6.963 44.875 1328 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.99 % Favored : 95.80 % Rotamer: Outliers : 3.46 % Allowed : 15.03 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.28), residues: 952 helix: 2.02 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -1.68 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 129 TYR 0.008 0.001 TYR A 335 PHE 0.013 0.001 PHE A 194 TRP 0.012 0.001 TRP A 197 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7692) covalent geometry : angle 0.59559 (10484) SS BOND : bond 0.00161 ( 2) SS BOND : angle 0.11326 ( 4) hydrogen bonds : bond 0.04767 ( 519) hydrogen bonds : angle 4.25897 ( 1551) link_NAG-ASN : bond 0.00018 ( 2) link_NAG-ASN : angle 1.37501 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.8559 (mmm) cc_final: 0.8181 (tpt) REVERT: B 320 LYS cc_start: 0.7936 (tttt) cc_final: 0.7668 (mtpm) REVERT: B 340 THR cc_start: 0.8977 (m) cc_final: 0.8708 (m) REVERT: B 413 MET cc_start: 0.9083 (ttp) cc_final: 0.8720 (ttp) REVERT: A 320 LYS cc_start: 0.7912 (tttt) cc_final: 0.7662 (mtpm) REVERT: A 340 THR cc_start: 0.8970 (m) cc_final: 0.8696 (m) REVERT: A 413 MET cc_start: 0.9073 (ttp) cc_final: 0.8702 (ttp) outliers start: 26 outliers final: 15 residues processed: 98 average time/residue: 0.3310 time to fit residues: 35.3780 Evaluate side-chains 99 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 484 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 62 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 93 optimal weight: 6.9990 chunk 27 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN A 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103742 restraints weight = 9208.562| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.62 r_work: 0.2960 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7696 Z= 0.136 Angle : 0.575 7.458 10494 Z= 0.283 Chirality : 0.038 0.203 1244 Planarity : 0.004 0.034 1266 Dihedral : 6.624 40.118 1328 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.20 % Favored : 95.59 % Rotamer: Outliers : 3.19 % Allowed : 15.69 % Favored : 81.12 % 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 aren not related in a simple way. whole: 1.81 (0.28), residues: 952 helix: 2.08 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -1.59 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 129 TYR 0.007 0.001 TYR B 335 PHE 0.012 0.001 PHE A 194 TRP 0.011 0.001 TRP A 453 HIS 0.002 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7692) covalent geometry : angle 0.57448 (10484) SS BOND : bond 0.00140 ( 2) SS BOND : angle 0.20124 ( 4) hydrogen bonds : bond 0.04584 ( 519) hydrogen bonds : angle 4.15548 ( 1551) link_NAG-ASN : bond 0.00026 ( 2) link_NAG-ASN : angle 1.33699 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8487 (mm) REVERT: B 117 MET cc_start: 0.8522 (mmm) cc_final: 0.8265 (mmm) REVERT: B 320 LYS cc_start: 0.7774 (tttt) cc_final: 0.7440 (mtpm) REVERT: B 340 THR cc_start: 0.8862 (m) cc_final: 0.8600 (m) REVERT: B 391 ILE cc_start: 0.8470 (mm) cc_final: 0.8221 (mt) REVERT: B 413 MET cc_start: 0.9095 (ttp) cc_final: 0.8718 (ttp) REVERT: A 320 LYS cc_start: 0.7753 (tttt) cc_final: 0.7442 (mtpm) REVERT: A 340 THR cc_start: 0.8855 (m) cc_final: 0.8589 (m) REVERT: A 391 ILE cc_start: 0.8460 (mm) cc_final: 0.8214 (mt) REVERT: A 413 MET cc_start: 0.9032 (ttp) cc_final: 0.8601 (ttp) outliers start: 24 outliers final: 14 residues processed: 105 average time/residue: 0.3822 time to fit residues: 43.4138 Evaluate side-chains 93 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 0.0370 chunk 83 optimal weight: 0.9980 chunk 44 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 0.0980 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.136827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104020 restraints weight = 9313.049| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.65 r_work: 0.2984 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7696 Z= 0.120 Angle : 0.548 7.531 10494 Z= 0.270 Chirality : 0.037 0.136 1244 Planarity : 0.003 0.034 1266 Dihedral : 6.391 41.744 1328 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.20 % Favored : 95.59 % Rotamer: Outliers : 3.19 % Allowed : 15.29 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.28), residues: 952 helix: 2.20 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -1.64 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 129 TYR 0.008 0.001 TYR B 113 PHE 0.011 0.001 PHE A 194 TRP 0.010 0.001 TRP A 197 HIS 0.001 0.000 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7692) covalent geometry : angle 0.54703 (10484) SS BOND : bond 0.00135 ( 2) SS BOND : angle 0.18648 ( 4) hydrogen bonds : bond 0.04256 ( 519) hydrogen bonds : angle 4.06149 ( 1551) link_NAG-ASN : bond 0.00014 ( 2) link_NAG-ASN : angle 1.33807 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8435 (mm) REVERT: B 117 MET cc_start: 0.8401 (mmm) cc_final: 0.8026 (mmm) REVERT: B 320 LYS cc_start: 0.7815 (tttt) cc_final: 0.7492 (mtpm) REVERT: B 340 THR cc_start: 0.8818 (m) cc_final: 0.8559 (m) REVERT: B 413 MET cc_start: 0.9072 (ttp) cc_final: 0.8684 (ttp) REVERT: A 320 LYS cc_start: 0.7719 (tttt) cc_final: 0.7416 (mtpm) REVERT: A 340 THR cc_start: 0.8808 (m) cc_final: 0.8556 (m) REVERT: A 391 ILE cc_start: 0.8460 (mm) cc_final: 0.8163 (mt) REVERT: A 413 MET cc_start: 0.9033 (ttp) cc_final: 0.8616 (ttp) outliers start: 24 outliers final: 14 residues processed: 102 average time/residue: 0.3767 time to fit residues: 41.7400 Evaluate side-chains 101 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 484 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 94 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.102882 restraints weight = 9261.529| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.62 r_work: 0.2947 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7696 Z= 0.139 Angle : 0.573 7.034 10494 Z= 0.282 Chirality : 0.038 0.138 1244 Planarity : 0.003 0.033 1266 Dihedral : 6.335 45.362 1328 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.20 % Favored : 95.59 % Rotamer: Outliers : 3.19 % Allowed : 16.49 % Favored : 80.32 % 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 aren not related in a simple way. whole: 1.86 (0.28), residues: 952 helix: 2.14 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.61 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 129 TYR 0.008 0.001 TYR B 113 PHE 0.013 0.001 PHE A 194 TRP 0.010 0.001 TRP A 197 HIS 0.002 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7692) covalent geometry : angle 0.57266 (10484) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.24859 ( 4) hydrogen bonds : bond 0.04631 ( 519) hydrogen bonds : angle 4.08922 ( 1551) link_NAG-ASN : bond 0.00028 ( 2) link_NAG-ASN : angle 1.26527 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8395 (mm) REVERT: B 117 MET cc_start: 0.8564 (mmm) cc_final: 0.8142 (tpt) REVERT: B 320 LYS cc_start: 0.7725 (tttt) cc_final: 0.7404 (mtpm) REVERT: B 340 THR cc_start: 0.8849 (m) cc_final: 0.8587 (m) REVERT: B 391 ILE cc_start: 0.8440 (mm) cc_final: 0.8160 (mt) REVERT: B 413 MET cc_start: 0.9071 (ttp) cc_final: 0.8643 (ttp) REVERT: B 513 LYS cc_start: 0.7497 (pmtt) cc_final: 0.7277 (pmmt) REVERT: A 320 LYS cc_start: 0.7726 (tttt) cc_final: 0.7437 (mtpm) REVERT: A 340 THR cc_start: 0.8829 (m) cc_final: 0.8572 (m) REVERT: A 391 ILE cc_start: 0.8469 (mm) cc_final: 0.8184 (mt) REVERT: A 413 MET cc_start: 0.9053 (ttp) cc_final: 0.8620 (ttp) REVERT: A 513 LYS cc_start: 0.7500 (pmtt) cc_final: 0.7278 (pmmt) outliers start: 24 outliers final: 13 residues processed: 93 average time/residue: 0.3394 time to fit residues: 34.3118 Evaluate side-chains 90 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 464 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.137541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.105357 restraints weight = 9282.869| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.60 r_work: 0.2962 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7696 Z= 0.131 Angle : 0.560 7.370 10494 Z= 0.276 Chirality : 0.038 0.137 1244 Planarity : 0.003 0.033 1266 Dihedral : 6.224 49.615 1328 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.78 % Favored : 96.01 % Rotamer: Outliers : 2.93 % Allowed : 16.76 % Favored : 80.32 % 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 aren not related in a simple way. whole: 1.86 (0.28), residues: 952 helix: 2.15 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.62 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 129 TYR 0.008 0.001 TYR B 113 PHE 0.012 0.001 PHE A 194 TRP 0.013 0.001 TRP A 453 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7692) covalent geometry : angle 0.55923 (10484) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.23743 ( 4) hydrogen bonds : bond 0.04422 ( 519) hydrogen bonds : angle 4.07391 ( 1551) link_NAG-ASN : bond 0.00013 ( 2) link_NAG-ASN : angle 1.17363 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8354 (mm) REVERT: B 320 LYS cc_start: 0.7766 (tttt) cc_final: 0.7457 (mtpm) REVERT: B 340 THR cc_start: 0.8850 (m) cc_final: 0.8598 (m) REVERT: B 391 ILE cc_start: 0.8460 (mm) cc_final: 0.8190 (mt) REVERT: B 413 MET cc_start: 0.9073 (ttp) cc_final: 0.8664 (ttp) REVERT: A 320 LYS cc_start: 0.7718 (tttt) cc_final: 0.7446 (mtpm) REVERT: A 340 THR cc_start: 0.8831 (m) cc_final: 0.8569 (m) REVERT: A 391 ILE cc_start: 0.8457 (mm) cc_final: 0.8181 (mt) REVERT: A 413 MET cc_start: 0.9045 (ttp) cc_final: 0.8621 (ttp) outliers start: 22 outliers final: 13 residues processed: 92 average time/residue: 0.3669 time to fit residues: 36.4885 Evaluate side-chains 90 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 464 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.138260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106219 restraints weight = 9148.524| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.58 r_work: 0.2971 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7696 Z= 0.125 Angle : 0.553 7.535 10494 Z= 0.273 Chirality : 0.037 0.135 1244 Planarity : 0.003 0.035 1266 Dihedral : 6.143 53.082 1328 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 2.26 % Allowed : 17.55 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.28), residues: 952 helix: 2.07 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -1.92 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 129 TYR 0.008 0.001 TYR B 113 PHE 0.011 0.001 PHE A 194 TRP 0.018 0.001 TRP A 453 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7692) covalent geometry : angle 0.55298 (10484) SS BOND : bond 0.00110 ( 2) SS BOND : angle 0.27681 ( 4) hydrogen bonds : bond 0.04322 ( 519) hydrogen bonds : angle 4.06180 ( 1551) link_NAG-ASN : bond 0.00006 ( 2) link_NAG-ASN : angle 1.18700 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 320 LYS cc_start: 0.7805 (tttt) cc_final: 0.7432 (mtpm) REVERT: B 340 THR cc_start: 0.8825 (m) cc_final: 0.8576 (m) REVERT: B 391 ILE cc_start: 0.8435 (mm) cc_final: 0.8164 (mt) REVERT: B 413 MET cc_start: 0.9083 (ttp) cc_final: 0.8676 (ttp) REVERT: B 513 LYS cc_start: 0.7606 (pmtt) cc_final: 0.7388 (pmmt) REVERT: A 320 LYS cc_start: 0.7724 (tttt) cc_final: 0.7364 (mtpm) REVERT: A 340 THR cc_start: 0.8816 (m) cc_final: 0.8557 (m) REVERT: A 391 ILE cc_start: 0.8425 (mm) cc_final: 0.8154 (mt) REVERT: A 413 MET cc_start: 0.9047 (ttp) cc_final: 0.8628 (ttp) REVERT: A 513 LYS cc_start: 0.7617 (pmtt) cc_final: 0.7398 (pmmt) outliers start: 17 outliers final: 13 residues processed: 84 average time/residue: 0.4493 time to fit residues: 40.6741 Evaluate side-chains 85 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 464 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 GLN A 457 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.106450 restraints weight = 9105.956| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.58 r_work: 0.2950 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7696 Z= 0.135 Angle : 0.559 5.853 10494 Z= 0.276 Chirality : 0.038 0.137 1244 Planarity : 0.003 0.035 1266 Dihedral : 6.152 55.995 1328 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.39 % Allowed : 17.55 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.28), residues: 952 helix: 2.11 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.62 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 129 TYR 0.009 0.001 TYR B 113 PHE 0.012 0.001 PHE A 194 TRP 0.018 0.001 TRP B 453 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7692) covalent geometry : angle 0.55852 (10484) SS BOND : bond 0.00104 ( 2) SS BOND : angle 0.27599 ( 4) hydrogen bonds : bond 0.04515 ( 519) hydrogen bonds : angle 4.07748 ( 1551) link_NAG-ASN : bond 0.00009 ( 2) link_NAG-ASN : angle 1.13513 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8255 (tp) REVERT: B 117 MET cc_start: 0.8116 (tpt) cc_final: 0.7761 (tpt) REVERT: B 320 LYS cc_start: 0.7712 (tttt) cc_final: 0.7322 (mtpm) REVERT: B 340 THR cc_start: 0.8856 (m) cc_final: 0.8598 (m) REVERT: B 391 ILE cc_start: 0.8447 (mm) cc_final: 0.8185 (mt) REVERT: B 413 MET cc_start: 0.9079 (ttp) cc_final: 0.8653 (ttp) REVERT: B 513 LYS cc_start: 0.7613 (pmtt) cc_final: 0.7406 (pmmt) REVERT: A 320 LYS cc_start: 0.7696 (tttt) cc_final: 0.7360 (mtpm) REVERT: A 340 THR cc_start: 0.8839 (m) cc_final: 0.8582 (m) REVERT: A 391 ILE cc_start: 0.8447 (mm) cc_final: 0.8184 (mt) REVERT: A 413 MET cc_start: 0.9052 (ttp) cc_final: 0.8622 (ttp) REVERT: A 513 LYS cc_start: 0.7616 (pmtt) cc_final: 0.7405 (pmmt) outliers start: 18 outliers final: 14 residues processed: 88 average time/residue: 0.4371 time to fit residues: 41.6313 Evaluate side-chains 89 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 464 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.097581 restraints weight = 9338.158| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.73 r_work: 0.2948 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7696 Z= 0.124 Angle : 0.543 5.621 10494 Z= 0.269 Chirality : 0.037 0.134 1244 Planarity : 0.003 0.033 1266 Dihedral : 6.033 58.873 1328 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.99 % Allowed : 18.09 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.28), residues: 952 helix: 2.06 (0.20), residues: 714 sheet: None (None), residues: 0 loop : -1.92 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 129 TYR 0.009 0.001 TYR B 113 PHE 0.011 0.001 PHE A 194 TRP 0.015 0.001 TRP B 453 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7692) covalent geometry : angle 0.54288 (10484) SS BOND : bond 0.00093 ( 2) SS BOND : angle 0.31470 ( 4) hydrogen bonds : bond 0.04270 ( 519) hydrogen bonds : angle 4.04620 ( 1551) link_NAG-ASN : bond 0.00010 ( 2) link_NAG-ASN : angle 1.14805 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2150.66 seconds wall clock time: 37 minutes 26.45 seconds (2246.45 seconds total)