Starting phenix.real_space_refine on Mon Apr 28 14:37:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzs_36752/04_2025/8jzs_36752.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzs_36752/04_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_36752/04_2025/8jzs_36752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzs_36752/04_2025/8jzs_36752.map" model { file = "/net/cci-nas-00/data/ceres_data/8jzs_36752/04_2025/8jzs_36752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzs_36752/04_2025/8jzs_36752.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'TYR:plan': 1, 'ARG:plan': 2} 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: {'TYR:plan': 1, 'ARG:plan': 2} 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: 5.28, per 1000 atoms: 0.70 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: 2.12 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.74 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: 2.13 Time building geometry restraints manager: 2.48 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.930 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.980 Find NCS groups from input model: 0.140 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:14.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.550 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP B 452 HIS 0.002 0.001 HIS A 348 PHE 0.021 0.001 PHE A 237 TYR 0.015 0.001 TYR B 335 ARG 0.004 0.000 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 2) link_NAG-ASN : angle 9.73488 ( 6) hydrogen bonds : bond 0.16320 ( 519) hydrogen bonds : angle 6.48046 ( 1551) SS BOND : bond 0.00292 ( 2) SS BOND : angle 0.40998 ( 4) covalent geometry : bond 0.00754 ( 7692) covalent geometry : angle 0.93070 (10484) *********************** 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 : 0.778 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: 0.7071 time to fit residues: 115.5999 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 : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 0.0570 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 45 optimal weight: 0.0570 chunk 56 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 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 = 48)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110392 restraints weight = 9348.773| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.76 r_work: 0.3128 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP A 453 HIS 0.003 0.001 HIS A 362 PHE 0.018 0.001 PHE A 240 TYR 0.007 0.001 TYR B 458 ARG 0.003 0.001 ARG B 33 Details of bonding type rmsd link_NAG-ASN : bond 0.00045 ( 2) link_NAG-ASN : angle 2.89555 ( 6) hydrogen bonds : bond 0.04564 ( 519) hydrogen bonds : angle 4.43245 ( 1551) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.33992 ( 4) covalent geometry : bond 0.00299 ( 7692) covalent geometry : angle 0.62119 (10484) *********************** 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 : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 THR cc_start: 0.8934 (m) cc_final: 0.8668 (m) REVERT: B 413 MET cc_start: 0.9085 (ttp) cc_final: 0.8725 (ttp) REVERT: A 222 PHE cc_start: 0.8377 (m-80) cc_final: 0.8154 (m-80) REVERT: A 340 THR cc_start: 0.8930 (m) cc_final: 0.8667 (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: 0.8464 time to fit residues: 96.3000 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 : 0.778 ------------------------------------------------------------------------------- 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 58 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.128029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.093508 restraints weight = 9444.560| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.75 r_work: 0.2875 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7696 Z= 0.224 Angle : 0.704 6.637 10494 Z= 0.350 Chirality : 0.044 0.242 1244 Planarity : 0.005 0.057 1266 Dihedral : 7.687 51.883 1328 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.41 % Favored : 95.38 % Rotamer: Outliers : 3.86 % Allowed : 11.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.28), residues: 952 helix: 1.67 (0.19), residues: 704 sheet: None (None), residues: 0 loop : -1.68 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 197 HIS 0.004 0.001 HIS A 362 PHE 0.015 0.002 PHE A 194 TYR 0.030 0.002 TYR A 113 ARG 0.003 0.001 ARG B 393 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 2) link_NAG-ASN : angle 1.51210 ( 6) hydrogen bonds : bond 0.06280 ( 519) hydrogen bonds : angle 4.56075 ( 1551) SS BOND : bond 0.00156 ( 2) SS BOND : angle 0.25698 ( 4) covalent geometry : bond 0.00548 ( 7692) covalent geometry : angle 0.70300 (10484) *********************** 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 126 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.8608 (mmm) cc_final: 0.8185 (tpt) REVERT: B 320 LYS cc_start: 0.7736 (tttt) cc_final: 0.7392 (mtpm) REVERT: B 340 THR cc_start: 0.8931 (m) cc_final: 0.8667 (m) REVERT: B 413 MET cc_start: 0.9091 (ttp) cc_final: 0.8680 (ttp) REVERT: B 513 LYS cc_start: 0.7491 (pmtt) cc_final: 0.7260 (pmmt) REVERT: A 117 MET cc_start: 0.8639 (mmm) cc_final: 0.8417 (tpt) REVERT: A 320 LYS cc_start: 0.7732 (tttt) cc_final: 0.7371 (mtpm) REVERT: A 340 THR cc_start: 0.8936 (m) cc_final: 0.8664 (m) REVERT: A 413 MET cc_start: 0.9109 (ttp) cc_final: 0.8708 (ttp) REVERT: A 513 LYS cc_start: 0.7489 (pmtt) cc_final: 0.7259 (pmmt) outliers start: 29 outliers final: 12 residues processed: 110 average time/residue: 0.7681 time to fit residues: 92.5230 Evaluate side-chains 95 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 112 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 376 LEU 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 240 PHE Chi-restraints excluded: chain A residue 429 LEU 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 49 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.135441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.102759 restraints weight = 9246.390| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.61 r_work: 0.2927 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7696 Z= 0.165 Angle : 0.627 7.816 10494 Z= 0.308 Chirality : 0.041 0.253 1244 Planarity : 0.004 0.035 1266 Dihedral : 7.205 45.872 1328 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.20 % Favored : 95.59 % Rotamer: Outliers : 3.86 % Allowed : 14.49 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.28), residues: 952 helix: 1.83 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -1.69 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 197 HIS 0.003 0.001 HIS A 362 PHE 0.014 0.001 PHE A 194 TYR 0.008 0.001 TYR A 335 ARG 0.002 0.000 ARG B 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 2) link_NAG-ASN : angle 1.34993 ( 6) hydrogen bonds : bond 0.05081 ( 519) hydrogen bonds : angle 4.35719 ( 1551) SS BOND : bond 0.00192 ( 2) SS BOND : angle 0.13577 ( 4) covalent geometry : bond 0.00391 ( 7692) covalent geometry : angle 0.62609 (10484) *********************** 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 119 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.8664 (mmm) cc_final: 0.8171 (tpt) REVERT: B 320 LYS cc_start: 0.7843 (tttt) cc_final: 0.7466 (mtpm) REVERT: B 340 THR cc_start: 0.8939 (m) cc_final: 0.8678 (m) REVERT: B 413 MET cc_start: 0.9065 (ttp) cc_final: 0.8642 (ttp) REVERT: A 320 LYS cc_start: 0.7818 (tttt) cc_final: 0.7475 (mtpm) REVERT: A 340 THR cc_start: 0.8941 (m) cc_final: 0.8676 (m) REVERT: A 413 MET cc_start: 0.9052 (ttp) cc_final: 0.8617 (ttp) outliers start: 29 outliers final: 18 residues processed: 102 average time/residue: 0.9332 time to fit residues: 103.3340 Evaluate side-chains 103 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain B residue 122 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 75 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 122 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 0.0470 chunk 86 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 overall best weight: 0.7880 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.129599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.095474 restraints weight = 9388.287| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.74 r_work: 0.2915 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7696 Z= 0.145 Angle : 0.597 7.196 10494 Z= 0.294 Chirality : 0.040 0.225 1244 Planarity : 0.004 0.034 1266 Dihedral : 6.854 41.347 1328 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.73 % Favored : 95.06 % Rotamer: Outliers : 3.72 % Allowed : 16.49 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.28), residues: 952 helix: 1.95 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -1.58 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 197 HIS 0.002 0.001 HIS A 348 PHE 0.013 0.001 PHE A 194 TYR 0.008 0.001 TYR A 52 ARG 0.002 0.000 ARG A 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00044 ( 2) link_NAG-ASN : angle 1.27755 ( 6) hydrogen bonds : bond 0.04804 ( 519) hydrogen bonds : angle 4.27521 ( 1551) SS BOND : bond 0.00168 ( 2) SS BOND : angle 0.15107 ( 4) covalent geometry : bond 0.00337 ( 7692) covalent geometry : angle 0.59669 (10484) *********************** 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 115 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8443 (mm) REVERT: B 117 MET cc_start: 0.8570 (mmm) cc_final: 0.8248 (mmm) REVERT: B 320 LYS cc_start: 0.7818 (tttt) cc_final: 0.7395 (mtpm) REVERT: B 340 THR cc_start: 0.8853 (m) cc_final: 0.8596 (m) REVERT: B 413 MET cc_start: 0.9063 (ttp) cc_final: 0.8653 (ttp) REVERT: B 513 LYS cc_start: 0.7473 (pmtt) cc_final: 0.7264 (pmmt) REVERT: A 320 LYS cc_start: 0.7754 (tttt) cc_final: 0.7408 (mtpm) REVERT: A 340 THR cc_start: 0.8874 (m) cc_final: 0.8616 (m) REVERT: A 413 MET cc_start: 0.9034 (ttp) cc_final: 0.8601 (ttp) outliers start: 28 outliers final: 18 residues processed: 100 average time/residue: 0.8738 time to fit residues: 94.7308 Evaluate side-chains 104 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 429 LEU 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 429 LEU Chi-restraints excluded: chain A residue 464 SER 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 4 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.129954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.095212 restraints weight = 9329.562| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.77 r_work: 0.2909 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7696 Z= 0.146 Angle : 0.588 7.209 10494 Z= 0.290 Chirality : 0.040 0.227 1244 Planarity : 0.004 0.035 1266 Dihedral : 6.688 42.499 1328 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.89 % Favored : 95.90 % Rotamer: Outliers : 3.19 % Allowed : 16.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.28), residues: 952 helix: 1.96 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -1.64 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 453 HIS 0.002 0.001 HIS A 348 PHE 0.013 0.001 PHE A 194 TYR 0.007 0.001 TYR A 52 ARG 0.001 0.000 ARG B 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00063 ( 2) link_NAG-ASN : angle 1.27615 ( 6) hydrogen bonds : bond 0.04818 ( 519) hydrogen bonds : angle 4.24637 ( 1551) SS BOND : bond 0.00165 ( 2) SS BOND : angle 0.19217 ( 4) covalent geometry : bond 0.00341 ( 7692) covalent geometry : angle 0.58784 (10484) *********************** 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 103 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8461 (mm) REVERT: B 117 MET cc_start: 0.8649 (mmm) cc_final: 0.8405 (mmm) REVERT: B 320 LYS cc_start: 0.7765 (tttt) cc_final: 0.7343 (mtpm) REVERT: B 340 THR cc_start: 0.8849 (m) cc_final: 0.8591 (m) REVERT: B 413 MET cc_start: 0.9073 (ttp) cc_final: 0.8654 (ttp) REVERT: A 320 LYS cc_start: 0.7693 (tttt) cc_final: 0.7338 (mtpm) REVERT: A 340 THR cc_start: 0.8870 (m) cc_final: 0.8608 (m) REVERT: A 413 MET cc_start: 0.9052 (ttp) cc_final: 0.8623 (ttp) outliers start: 24 outliers final: 17 residues processed: 92 average time/residue: 1.4410 time to fit residues: 142.6877 Evaluate side-chains 95 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 429 LEU 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 122 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 464 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.136612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.104382 restraints weight = 9074.140| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.58 r_work: 0.2948 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3527 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= 0.136 Angle : 0.567 6.570 10494 Z= 0.280 Chirality : 0.038 0.136 1244 Planarity : 0.003 0.035 1266 Dihedral : 6.489 47.415 1328 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.41 % Favored : 95.38 % Rotamer: Outliers : 3.59 % Allowed : 16.89 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.28), residues: 952 helix: 2.02 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -1.67 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 453 HIS 0.002 0.001 HIS A 348 PHE 0.012 0.001 PHE A 194 TYR 0.007 0.001 TYR B 335 ARG 0.001 0.000 ARG A 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00033 ( 2) link_NAG-ASN : angle 1.20878 ( 6) hydrogen bonds : bond 0.04590 ( 519) hydrogen bonds : angle 4.18208 ( 1551) SS BOND : bond 0.00146 ( 2) SS BOND : angle 0.25396 ( 4) covalent geometry : bond 0.00312 ( 7692) covalent geometry : angle 0.56661 (10484) *********************** 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 107 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8512 (mm) REVERT: B 320 LYS cc_start: 0.7814 (tttt) cc_final: 0.7431 (mtpm) REVERT: B 340 THR cc_start: 0.8869 (m) cc_final: 0.8609 (m) REVERT: B 413 MET cc_start: 0.9057 (ttp) cc_final: 0.8631 (ttp) REVERT: A 320 LYS cc_start: 0.7727 (tttt) cc_final: 0.7405 (mtpm) REVERT: A 340 THR cc_start: 0.8897 (m) cc_final: 0.8622 (m) REVERT: A 413 MET cc_start: 0.9067 (ttp) cc_final: 0.8657 (ttp) REVERT: A 513 LYS cc_start: 0.7468 (pmtt) cc_final: 0.7262 (pmmt) outliers start: 27 outliers final: 20 residues processed: 93 average time/residue: 0.8018 time to fit residues: 81.2506 Evaluate side-chains 98 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 430 VAL 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 122 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 VAL 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 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.134502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.102035 restraints weight = 9254.573| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.59 r_work: 0.2911 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.004 0.043 7696 Z= 0.158 Angle : 0.589 5.655 10494 Z= 0.291 Chirality : 0.039 0.141 1244 Planarity : 0.004 0.036 1266 Dihedral : 6.570 50.492 1328 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.10 % Favored : 95.69 % Rotamer: Outliers : 3.86 % Allowed : 16.76 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.28), residues: 952 helix: 1.96 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -1.76 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 453 HIS 0.003 0.001 HIS A 348 PHE 0.013 0.001 PHE A 194 TYR 0.008 0.001 TYR B 113 ARG 0.001 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 2) link_NAG-ASN : angle 1.13308 ( 6) hydrogen bonds : bond 0.05043 ( 519) hydrogen bonds : angle 4.24200 ( 1551) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.19972 ( 4) covalent geometry : bond 0.00379 ( 7692) covalent geometry : angle 0.58831 (10484) *********************** 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 104 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8373 (mm) REVERT: B 320 LYS cc_start: 0.7846 (tttt) cc_final: 0.7442 (mtpm) REVERT: B 340 THR cc_start: 0.8893 (m) cc_final: 0.8632 (m) REVERT: B 413 MET cc_start: 0.9073 (ttp) cc_final: 0.8631 (ttp) REVERT: A 320 LYS cc_start: 0.7694 (tttt) cc_final: 0.7372 (mtpm) REVERT: A 340 THR cc_start: 0.8922 (m) cc_final: 0.8645 (m) REVERT: A 413 MET cc_start: 0.9098 (ttp) cc_final: 0.8667 (ttp) REVERT: A 513 LYS cc_start: 0.7494 (pmtt) cc_final: 0.7289 (pmmt) outliers start: 29 outliers final: 23 residues processed: 91 average time/residue: 1.0764 time to fit residues: 105.7774 Evaluate side-chains 95 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 461 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 122 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 429 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 76 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 67 optimal weight: 0.0870 chunk 31 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.0970 chunk 87 optimal weight: 0.7980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.137424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.105267 restraints weight = 9218.389| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.59 r_work: 0.2959 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7696 Z= 0.124 Angle : 0.549 6.564 10494 Z= 0.271 Chirality : 0.037 0.134 1244 Planarity : 0.003 0.034 1266 Dihedral : 6.309 55.858 1328 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.20 % Favored : 95.59 % Rotamer: Outliers : 2.93 % Allowed : 17.82 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.28), residues: 952 helix: 2.09 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.76 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 453 HIS 0.001 0.000 HIS A 362 PHE 0.011 0.001 PHE B 194 TYR 0.008 0.001 TYR B 335 ARG 0.001 0.000 ARG B 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00012 ( 2) link_NAG-ASN : angle 1.18089 ( 6) hydrogen bonds : bond 0.04376 ( 519) hydrogen bonds : angle 4.14258 ( 1551) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.27757 ( 4) covalent geometry : bond 0.00275 ( 7692) covalent geometry : angle 0.54844 (10484) *********************** 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 97 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8242 (tp) REVERT: B 340 THR cc_start: 0.8842 (m) cc_final: 0.8581 (m) REVERT: B 413 MET cc_start: 0.9065 (ttp) cc_final: 0.8645 (ttp) REVERT: B 513 LYS cc_start: 0.7456 (pmtt) cc_final: 0.6873 (tppp) REVERT: A 320 LYS cc_start: 0.7773 (tttt) cc_final: 0.7384 (mtpm) REVERT: A 340 THR cc_start: 0.8876 (m) cc_final: 0.8618 (m) REVERT: A 413 MET cc_start: 0.9048 (ttp) cc_final: 0.8627 (ttp) REVERT: A 513 LYS cc_start: 0.7475 (pmtt) cc_final: 0.6924 (tppp) outliers start: 22 outliers final: 17 residues processed: 87 average time/residue: 0.8994 time to fit residues: 85.1317 Evaluate side-chains 90 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 95 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 376 LEU 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 8 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 0.0060 chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3591 r_free = 0.3591 target = 0.136305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103991 restraints weight = 9170.048| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.60 r_work: 0.2941 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3724 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= 0.135 Angle : 0.560 5.640 10494 Z= 0.277 Chirality : 0.038 0.136 1244 Planarity : 0.003 0.034 1266 Dihedral : 6.260 57.850 1328 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.66 % Allowed : 18.35 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.28), residues: 952 helix: 2.07 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.77 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 453 HIS 0.003 0.001 HIS B 348 PHE 0.012 0.001 PHE A 194 TYR 0.008 0.001 TYR A 113 ARG 0.001 0.000 ARG B 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00018 ( 2) link_NAG-ASN : angle 1.16194 ( 6) hydrogen bonds : bond 0.04600 ( 519) hydrogen bonds : angle 4.15882 ( 1551) SS BOND : bond 0.00117 ( 2) SS BOND : angle 0.29460 ( 4) covalent geometry : bond 0.00312 ( 7692) covalent geometry : angle 0.55936 (10484) ********************** 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 90 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8249 (tp) REVERT: B 117 MET cc_start: 0.8212 (tpt) cc_final: 0.7909 (tpt) REVERT: B 340 THR cc_start: 0.8854 (m) cc_final: 0.8596 (m) REVERT: B 391 ILE cc_start: 0.8476 (mm) cc_final: 0.8205 (mt) REVERT: B 413 MET cc_start: 0.9105 (ttp) cc_final: 0.8686 (ttp) REVERT: B 513 LYS cc_start: 0.7467 (pmtt) cc_final: 0.7258 (pmmt) REVERT: A 320 LYS cc_start: 0.7776 (tttt) cc_final: 0.7384 (mtpm) REVERT: A 340 THR cc_start: 0.8875 (m) cc_final: 0.8614 (m) REVERT: A 413 MET cc_start: 0.9058 (ttp) cc_final: 0.8621 (ttp) REVERT: A 513 LYS cc_start: 0.7477 (pmtt) cc_final: 0.6922 (tppp) outliers start: 20 outliers final: 17 residues processed: 82 average time/residue: 0.8396 time to fit residues: 74.9472 Evaluate side-chains 87 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 95 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 376 LEU 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 85 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3455 r_free = 0.3455 target = 0.127322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.093148 restraints weight = 9300.070| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.73 r_work: 0.2881 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7696 Z= 0.166 Angle : 0.588 5.653 10494 Z= 0.291 Chirality : 0.040 0.139 1244 Planarity : 0.003 0.035 1266 Dihedral : 6.403 57.298 1328 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.53 % Allowed : 18.35 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.28), residues: 952 helix: 1.97 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.81 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 453 HIS 0.003 0.001 HIS B 348 PHE 0.013 0.001 PHE A 194 TYR 0.008 0.001 TYR A 113 ARG 0.002 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00047 ( 2) link_NAG-ASN : angle 1.10346 ( 6) hydrogen bonds : bond 0.05093 ( 519) hydrogen bonds : angle 4.24761 ( 1551) SS BOND : bond 0.00120 ( 2) SS BOND : angle 0.21398 ( 4) covalent geometry : bond 0.00403 ( 7692) covalent geometry : angle 0.58717 (10484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5218.08 seconds wall clock time: 91 minutes 51.66 seconds (5511.66 seconds total)