Starting phenix.real_space_refine on Sun May 11 07:11:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzs_36752/05_2025/8jzs_36752.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzs_36752/05_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_36752/05_2025/8jzs_36752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzs_36752/05_2025/8jzs_36752.map" model { file = "/net/cci-nas-00/data/ceres_data/8jzs_36752/05_2025/8jzs_36752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzs_36752/05_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-5687/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: 5.00, per 1000 atoms: 0.67 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: 2.26 Conformation dependent library (CDL) restraints added in 933.5 milliseconds 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: 0.69 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: 1.98 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: 0.730 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.580 Find NCS groups from input model: 0.110 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:10.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.320 ------------------------------------------------------------------------------- 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 : 0.749 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: 0.6616 time to fit residues: 108.1658 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 : 0.715 ------------------------------------------------------------------------------- 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 = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110393 restraints weight = 9348.774| |-----------------------------------------------------------------------------| 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: 0.7944 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 : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 THR cc_start: 0.8935 (m) cc_final: 0.8669 (m) REVERT: B 413 MET cc_start: 0.9085 (ttp) cc_final: 0.8724 (ttp) REVERT: A 222 PHE cc_start: 0.8378 (m-80) cc_final: 0.8154 (m-80) REVERT: A 340 THR cc_start: 0.8931 (m) cc_final: 0.8667 (m) REVERT: A 413 MET cc_start: 0.9068 (ttp) cc_final: 0.8689 (ttp) outliers start: 12 outliers final: 2 residues processed: 105 average time/residue: 0.7977 time to fit residues: 90.8537 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 : 0.736 ------------------------------------------------------------------------------- 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: 0.7980 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 79 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.133355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.099494 restraints weight = 9354.014| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.69 r_work: 0.2957 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7696 Z= 0.166 Angle : 0.632 7.020 10494 Z= 0.314 Chirality : 0.041 0.184 1244 Planarity : 0.004 0.052 1266 Dihedral : 7.107 47.583 1328 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.41 % Favored : 95.38 % Rotamer: Outliers : 4.12 % Allowed : 11.70 % Favored : 84.18 % 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: 1.92 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -1.60 (0.43), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 197 HIS 0.003 0.001 HIS B 348 PHE 0.012 0.002 PHE A 194 TYR 0.020 0.002 TYR B 113 ARG 0.003 0.001 ARG B 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 2) link_NAG-ASN : angle 1.63549 ( 6) hydrogen bonds : bond 0.05253 ( 519) hydrogen bonds : angle 4.33954 ( 1551) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.33016 ( 4) covalent geometry : bond 0.00391 ( 7692) covalent geometry : angle 0.63134 (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 128 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.8476 (mmm) cc_final: 0.8157 (tpt) REVERT: B 320 LYS cc_start: 0.7787 (tttt) cc_final: 0.7493 (mtpm) REVERT: B 340 THR cc_start: 0.8891 (m) cc_final: 0.8610 (m) REVERT: B 413 MET cc_start: 0.9095 (ttp) cc_final: 0.8699 (ttp) REVERT: B 513 LYS cc_start: 0.7433 (pmtt) cc_final: 0.7230 (pmmt) REVERT: A 320 LYS cc_start: 0.7770 (tttt) cc_final: 0.7485 (mtpm) REVERT: A 340 THR cc_start: 0.8890 (m) cc_final: 0.8622 (m) REVERT: A 413 MET cc_start: 0.9079 (ttp) cc_final: 0.8672 (ttp) REVERT: A 513 LYS cc_start: 0.7486 (pmtt) cc_final: 0.7285 (pmmt) outliers start: 31 outliers final: 14 residues processed: 110 average time/residue: 0.7447 time to fit residues: 89.7856 Evaluate side-chains 98 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 B residue 526 ASN 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 371 MET Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 526 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 0.0980 chunk 71 optimal weight: 0.0670 chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.135468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102465 restraints weight = 9313.254| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.63 r_work: 0.2942 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7696 Z= 0.160 Angle : 0.611 7.532 10494 Z= 0.300 Chirality : 0.041 0.216 1244 Planarity : 0.004 0.035 1266 Dihedral : 6.877 42.703 1328 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.99 % Favored : 95.80 % Rotamer: Outliers : 3.59 % Allowed : 15.16 % Favored : 81.25 % 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: 1.69 (0.28), residues: 952 helix: 1.97 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -1.52 (0.43), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 197 HIS 0.003 0.001 HIS A 348 PHE 0.013 0.001 PHE A 194 TYR 0.017 0.001 TYR A 113 ARG 0.002 0.001 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00053 ( 2) link_NAG-ASN : angle 1.37192 ( 6) hydrogen bonds : bond 0.04936 ( 519) hydrogen bonds : angle 4.26883 ( 1551) SS BOND : bond 0.00179 ( 2) SS BOND : angle 0.16231 ( 4) covalent geometry : bond 0.00382 ( 7692) covalent geometry : angle 0.61084 (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 116 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.8505 (mmm) cc_final: 0.8162 (tpt) REVERT: B 320 LYS cc_start: 0.7781 (tttt) cc_final: 0.7468 (mtpm) REVERT: B 340 THR cc_start: 0.8900 (m) cc_final: 0.8631 (m) REVERT: B 413 MET cc_start: 0.9077 (ttp) cc_final: 0.8676 (ttp) REVERT: A 320 LYS cc_start: 0.7802 (tttt) cc_final: 0.7491 (mtpm) REVERT: A 340 THR cc_start: 0.8880 (m) cc_final: 0.8606 (m) REVERT: A 413 MET cc_start: 0.9059 (ttp) cc_final: 0.8647 (ttp) outliers start: 27 outliers final: 14 residues processed: 99 average time/residue: 0.7524 time to fit residues: 81.3997 Evaluate side-chains 96 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 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 207 ILE 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: 2.9990 chunk 50 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.135489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102463 restraints weight = 9228.210| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.64 r_work: 0.2939 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7696 Z= 0.151 Angle : 0.598 7.565 10494 Z= 0.294 Chirality : 0.039 0.227 1244 Planarity : 0.004 0.035 1266 Dihedral : 6.753 40.704 1328 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.41 % Favored : 95.38 % Rotamer: Outliers : 2.79 % Allowed : 15.29 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.01 (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 0.011 0.001 TRP A 453 HIS 0.002 0.001 HIS A 362 PHE 0.013 0.001 PHE A 194 TYR 0.007 0.001 TYR A 52 ARG 0.001 0.000 ARG B 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00048 ( 2) link_NAG-ASN : angle 1.29367 ( 6) hydrogen bonds : bond 0.04894 ( 519) hydrogen bonds : angle 4.23240 ( 1551) SS BOND : bond 0.00173 ( 2) SS BOND : angle 0.09115 ( 4) covalent geometry : bond 0.00355 ( 7692) covalent geometry : angle 0.59735 (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 107 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8381 (mm) REVERT: B 117 MET cc_start: 0.8475 (mmm) cc_final: 0.8104 (tpt) REVERT: B 320 LYS cc_start: 0.7797 (tttt) cc_final: 0.7458 (mtpm) REVERT: B 340 THR cc_start: 0.8891 (m) cc_final: 0.8632 (m) REVERT: B 413 MET cc_start: 0.9090 (ttp) cc_final: 0.8687 (ttp) REVERT: A 320 LYS cc_start: 0.7766 (tttt) cc_final: 0.7446 (mtpm) REVERT: A 340 THR cc_start: 0.8869 (m) cc_final: 0.8610 (m) REVERT: A 391 ILE cc_start: 0.8504 (mm) cc_final: 0.8240 (mt) REVERT: A 413 MET cc_start: 0.9064 (ttp) cc_final: 0.8639 (ttp) outliers start: 21 outliers final: 13 residues processed: 100 average time/residue: 0.8402 time to fit residues: 91.0732 Evaluate side-chains 93 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 84 LEU Chi-restraints excluded: chain B residue 118 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 464 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 207 ILE 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 4 optimal weight: 0.6980 chunk 15 optimal weight: 0.0670 chunk 90 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.098349 restraints weight = 9308.267| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.73 r_work: 0.2952 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7696 Z= 0.130 Angle : 0.562 7.203 10494 Z= 0.277 Chirality : 0.038 0.137 1244 Planarity : 0.003 0.034 1266 Dihedral : 6.394 43.955 1328 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.10 % Favored : 95.69 % Rotamer: Outliers : 3.59 % Allowed : 15.43 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.81 (0.28), residues: 952 helix: 2.11 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.65 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 197 HIS 0.002 0.001 HIS A 348 PHE 0.011 0.001 PHE A 194 TYR 0.007 0.001 TYR B 335 ARG 0.001 0.000 ARG B 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00013 ( 2) link_NAG-ASN : angle 1.29975 ( 6) hydrogen bonds : bond 0.04425 ( 519) hydrogen bonds : angle 4.12124 ( 1551) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.22833 ( 4) covalent geometry : bond 0.00295 ( 7692) covalent geometry : angle 0.56167 (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 111 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8340 (mm) REVERT: B 117 MET cc_start: 0.8343 (mmm) cc_final: 0.8008 (tpt) REVERT: B 320 LYS cc_start: 0.7708 (tttt) cc_final: 0.7360 (mtpm) REVERT: B 340 THR cc_start: 0.8802 (m) cc_final: 0.8555 (m) REVERT: B 413 MET cc_start: 0.9059 (ttp) cc_final: 0.8646 (ttp) REVERT: A 320 LYS cc_start: 0.7652 (tttt) cc_final: 0.7345 (mtpm) REVERT: A 340 THR cc_start: 0.8790 (m) cc_final: 0.8521 (m) REVERT: A 413 MET cc_start: 0.9038 (ttp) cc_final: 0.8613 (ttp) outliers start: 27 outliers final: 15 residues processed: 100 average time/residue: 0.8179 time to fit residues: 88.7580 Evaluate side-chains 97 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE 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 207 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 484 MET 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 371 MET Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 483 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 50 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 70 optimal weight: 0.0070 chunk 23 optimal weight: 8.9990 chunk 7 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.131932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.098234 restraints weight = 9325.385| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.73 r_work: 0.2953 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3332 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 : 0.552 7.110 10494 Z= 0.271 Chirality : 0.037 0.136 1244 Planarity : 0.003 0.034 1266 Dihedral : 6.291 46.693 1328 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.20 % Favored : 95.59 % Rotamer: Outliers : 3.06 % Allowed : 16.62 % 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 (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: 1.68 (0.28), residues: 952 helix: 2.05 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -1.97 (0.39), residues: 236 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 0.011 0.001 PHE A 194 TYR 0.007 0.001 TYR A 113 ARG 0.001 0.000 ARG A 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00006 ( 2) link_NAG-ASN : angle 1.28391 ( 6) hydrogen bonds : bond 0.04323 ( 519) hydrogen bonds : angle 4.07498 ( 1551) SS BOND : bond 0.00145 ( 2) SS BOND : angle 0.21871 ( 4) covalent geometry : bond 0.00278 ( 7692) covalent geometry : angle 0.55126 (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 103 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8330 (mm) REVERT: B 117 MET cc_start: 0.8310 (mmm) cc_final: 0.7985 (tpt) REVERT: B 320 LYS cc_start: 0.7766 (tttt) cc_final: 0.7430 (mtpm) REVERT: B 340 THR cc_start: 0.8804 (m) cc_final: 0.8550 (m) REVERT: B 391 ILE cc_start: 0.8434 (mm) cc_final: 0.8148 (mt) REVERT: B 413 MET cc_start: 0.9055 (ttp) cc_final: 0.8631 (ttp) REVERT: A 320 LYS cc_start: 0.7640 (tttt) cc_final: 0.7340 (mtpm) REVERT: A 340 THR cc_start: 0.8774 (m) cc_final: 0.8519 (m) REVERT: A 391 ILE cc_start: 0.8419 (mm) cc_final: 0.8130 (mt) REVERT: A 413 MET cc_start: 0.9042 (ttp) cc_final: 0.8620 (ttp) outliers start: 23 outliers final: 14 residues processed: 94 average time/residue: 0.8712 time to fit residues: 88.5993 Evaluate side-chains 94 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 84 LEU Chi-restraints excluded: chain B residue 118 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 B residue 484 MET 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 Chi-restraints excluded: chain A residue 484 MET 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: 0.8980 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.134412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101895 restraints weight = 9278.971| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.61 r_work: 0.2905 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7696 Z= 0.165 Angle : 0.591 5.652 10494 Z= 0.293 Chirality : 0.040 0.142 1244 Planarity : 0.004 0.035 1266 Dihedral : 6.510 49.080 1328 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.20 % Favored : 95.59 % Rotamer: Outliers : 3.06 % Allowed : 16.22 % Favored : 80.72 % 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: 1.62 (0.28), residues: 952 helix: 1.98 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.70 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 453 HIS 0.003 0.001 HIS A 348 PHE 0.014 0.001 PHE A 194 TYR 0.008 0.001 TYR A 52 ARG 0.002 0.000 ARG B 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00059 ( 2) link_NAG-ASN : angle 1.14838 ( 6) hydrogen bonds : bond 0.05152 ( 519) hydrogen bonds : angle 4.21712 ( 1551) SS BOND : bond 0.00151 ( 2) SS BOND : angle 0.20887 ( 4) covalent geometry : bond 0.00396 ( 7692) covalent geometry : angle 0.59040 (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 97 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8432 (mm) REVERT: B 117 MET cc_start: 0.8607 (mmm) cc_final: 0.8399 (tpt) REVERT: B 320 LYS cc_start: 0.7748 (tttt) cc_final: 0.7437 (mtpm) REVERT: B 340 THR cc_start: 0.8918 (m) cc_final: 0.8652 (m) REVERT: B 391 ILE cc_start: 0.8506 (mm) cc_final: 0.8229 (mt) REVERT: B 413 MET cc_start: 0.9129 (ttp) cc_final: 0.8702 (ttp) REVERT: B 513 LYS cc_start: 0.7507 (pmtt) cc_final: 0.7283 (pmmt) REVERT: A 320 LYS cc_start: 0.7714 (tttt) cc_final: 0.7424 (mtpm) REVERT: A 340 THR cc_start: 0.8908 (m) cc_final: 0.8647 (m) REVERT: A 391 ILE cc_start: 0.8522 (mm) cc_final: 0.8241 (mt) REVERT: A 413 MET cc_start: 0.9106 (ttp) cc_final: 0.8679 (ttp) REVERT: A 513 LYS cc_start: 0.7512 (pmtt) cc_final: 0.7282 (pmmt) outliers start: 23 outliers final: 16 residues processed: 91 average time/residue: 0.9041 time to fit residues: 89.1517 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 : 0.751 ------------------------------------------------------------------------------- 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 84 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 429 LEU 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 207 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 483 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: 6.9990 chunk 67 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.130540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.096799 restraints weight = 9451.104| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.74 r_work: 0.2927 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3567 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= 0.131 Angle : 0.557 5.643 10494 Z= 0.276 Chirality : 0.038 0.136 1244 Planarity : 0.003 0.034 1266 Dihedral : 6.328 54.265 1328 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.32 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 (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: 1.98 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -2.01 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 453 HIS 0.002 0.001 HIS A 362 PHE 0.012 0.001 PHE A 194 TYR 0.008 0.001 TYR A 335 ARG 0.001 0.000 ARG A 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00022 ( 2) link_NAG-ASN : angle 1.16874 ( 6) hydrogen bonds : bond 0.04508 ( 519) hydrogen bonds : angle 4.14246 ( 1551) SS BOND : bond 0.00139 ( 2) SS BOND : angle 0.21249 ( 4) covalent geometry : bond 0.00298 ( 7692) covalent geometry : angle 0.55701 (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 96 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8338 (mm) REVERT: B 117 MET cc_start: 0.8446 (mmm) cc_final: 0.8024 (tpt) REVERT: B 320 LYS cc_start: 0.7724 (tttt) cc_final: 0.7385 (mtpm) REVERT: B 340 THR cc_start: 0.8815 (m) cc_final: 0.8565 (m) REVERT: B 413 MET cc_start: 0.9098 (ttp) cc_final: 0.8686 (ttp) REVERT: B 465 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7747 (pt0) REVERT: B 513 LYS cc_start: 0.7516 (pmtt) cc_final: 0.7301 (pmmt) REVERT: A 320 LYS cc_start: 0.7660 (tttt) cc_final: 0.7280 (mtpm) REVERT: A 340 THR cc_start: 0.8822 (m) cc_final: 0.8570 (m) REVERT: A 391 ILE cc_start: 0.8435 (mm) cc_final: 0.8147 (mt) REVERT: A 413 MET cc_start: 0.9050 (ttp) cc_final: 0.8617 (ttp) REVERT: A 513 LYS cc_start: 0.7516 (pmtt) cc_final: 0.7296 (pmmt) outliers start: 24 outliers final: 14 residues processed: 88 average time/residue: 0.8766 time to fit residues: 84.1876 Evaluate side-chains 86 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 24 optimal weight: 0.0170 chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.131411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.098028 restraints weight = 9385.500| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.73 r_work: 0.2946 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3629 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= 0.122 Angle : 0.540 5.688 10494 Z= 0.267 Chirality : 0.037 0.135 1244 Planarity : 0.003 0.035 1266 Dihedral : 6.110 58.479 1328 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.13 % Allowed : 17.69 % 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 (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: 1.60 (0.28), residues: 952 helix: 2.00 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -2.03 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 453 HIS 0.002 0.001 HIS A 348 PHE 0.011 0.001 PHE A 194 TYR 0.009 0.001 TYR B 113 ARG 0.001 0.000 ARG A 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00008 ( 2) link_NAG-ASN : angle 1.17159 ( 6) hydrogen bonds : bond 0.04244 ( 519) hydrogen bonds : angle 4.05759 ( 1551) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.34614 ( 4) covalent geometry : bond 0.00274 ( 7692) covalent geometry : angle 0.53923 (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: 16 poor density : 74 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8297 (mm) REVERT: B 117 MET cc_start: 0.8433 (mmm) cc_final: 0.7990 (tpt) REVERT: B 320 LYS cc_start: 0.7754 (tttt) cc_final: 0.7428 (mtpm) REVERT: B 340 THR cc_start: 0.8789 (m) cc_final: 0.8549 (m) REVERT: B 413 MET cc_start: 0.9091 (ttp) cc_final: 0.8675 (ttp) REVERT: B 513 LYS cc_start: 0.7495 (pmtt) cc_final: 0.7291 (pmmt) REVERT: A 320 LYS cc_start: 0.7629 (tttt) cc_final: 0.7279 (mtpm) REVERT: A 340 THR cc_start: 0.8804 (m) cc_final: 0.8558 (m) REVERT: A 391 ILE cc_start: 0.8416 (mm) cc_final: 0.8145 (mt) REVERT: A 413 MET cc_start: 0.9043 (ttp) cc_final: 0.8611 (ttp) REVERT: A 513 LYS cc_start: 0.7488 (pmtt) cc_final: 0.7282 (pmmt) outliers start: 16 outliers final: 15 residues processed: 87 average time/residue: 0.8657 time to fit residues: 81.6337 Evaluate side-chains 89 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 430 VAL 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 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: 3.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 86 optimal weight: 0.0370 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.097255 restraints weight = 9257.302| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.73 r_work: 0.2940 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3663 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= 0.126 Angle : 0.543 5.613 10494 Z= 0.269 Chirality : 0.037 0.134 1244 Planarity : 0.003 0.035 1266 Dihedral : 6.073 59.421 1328 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.39 % Allowed : 17.42 % 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 (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: 1.60 (0.28), residues: 952 helix: 2.01 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -2.04 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 453 HIS 0.002 0.001 HIS A 348 PHE 0.011 0.001 PHE A 194 TYR 0.008 0.001 TYR B 113 ARG 0.001 0.000 ARG B 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00011 ( 2) link_NAG-ASN : angle 1.14766 ( 6) hydrogen bonds : bond 0.04326 ( 519) hydrogen bonds : angle 4.05508 ( 1551) SS BOND : bond 0.00087 ( 2) SS BOND : angle 0.33878 ( 4) covalent geometry : bond 0.00287 ( 7692) covalent geometry : angle 0.54262 (10484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4835.59 seconds wall clock time: 84 minutes 1.40 seconds (5041.40 seconds total)