Starting phenix.real_space_refine on Fri Jul 19 11:10:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzs_36752/07_2024/8jzs_36752.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzs_36752/07_2024/8jzs_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzs_36752/07_2024/8jzs_36752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzs_36752/07_2024/8jzs_36752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzs_36752/07_2024/8jzs_36752.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzs_36752/07_2024/8jzs_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 Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.69, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 2.68 Conformation dependent library (CDL) restraints added in 1.5 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: 0.60 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: 1.89 Time building geometry restraints manager: 2.96 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: 97.47 - 104.79: 157 104.79 - 112.11: 3908 112.11 - 119.43: 2459 119.43 - 126.75: 3841 126.75 - 134.07: 119 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 2.520 nonbonded pdb=" OE2 GLU B 309 " pdb=" NZ LYS B 311 " model vdw 2.364 2.520 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG SER A 255 " model vdw 2.373 2.440 ... (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 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: 2.400 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.260 Find NCS groups from input model: 0.250 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:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.210 ------------------------------------------------------------------------------- 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 7692 Z= 0.491 Angle : 0.931 10.311 10484 Z= 0.505 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.770 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: 0.7091 time to fit residues: 115.5902 Evaluate side-chains 90 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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: 3.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 49 optimal weight: 0.0570 chunk 38 optimal weight: 0.0570 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.0070 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.4234 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7692 Z= 0.193 Angle : 0.620 8.152 10484 Z= 0.305 Chirality : 0.039 0.145 1244 Planarity : 0.005 0.064 1266 Dihedral : 8.097 54.617 1328 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.57 % Favored : 96.22 % Rotamer: Outliers : 1.60 % Allowed : 9.31 % Favored : 89.10 % 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: 1.22 (0.28), residues: 952 helix: 1.65 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -1.85 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 453 HIS 0.002 0.001 HIS A 362 PHE 0.018 0.001 PHE A 240 TYR 0.007 0.001 TYR B 458 ARG 0.002 0.000 ARG A 34 *********************** 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 111 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 THR cc_start: 0.8931 (m) cc_final: 0.8622 (m) REVERT: B 413 MET cc_start: 0.8595 (ttp) cc_final: 0.8322 (ttp) REVERT: A 340 THR cc_start: 0.8925 (m) cc_final: 0.8615 (m) REVERT: A 413 MET cc_start: 0.8567 (ttp) cc_final: 0.8291 (ttp) outliers start: 12 outliers final: 4 residues processed: 103 average time/residue: 0.7850 time to fit residues: 88.1640 Evaluate side-chains 98 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 511 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 0.0030 overall best weight: 1.4074 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.005 0.056 7692 Z= 0.310 Angle : 0.658 6.458 10484 Z= 0.326 Chirality : 0.043 0.246 1244 Planarity : 0.005 0.064 1266 Dihedral : 7.550 51.484 1328 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.99 % Favored : 95.80 % Rotamer: Outliers : 3.72 % Allowed : 11.70 % Favored : 84.57 % 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: 1.43 (0.28), residues: 952 helix: 1.79 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -1.61 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.004 0.001 HIS A 362 PHE 0.014 0.002 PHE A 194 TYR 0.026 0.002 TYR A 113 ARG 0.002 0.001 ARG A 404 *********************** 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 120 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.8552 (mmm) cc_final: 0.8157 (tpt) REVERT: B 340 THR cc_start: 0.8916 (m) cc_final: 0.8611 (m) REVERT: B 413 MET cc_start: 0.8569 (ttp) cc_final: 0.8250 (ttp) REVERT: A 340 THR cc_start: 0.8902 (m) cc_final: 0.8592 (m) REVERT: A 413 MET cc_start: 0.8588 (ttp) cc_final: 0.8272 (ttp) outliers start: 28 outliers final: 8 residues processed: 103 average time/residue: 0.7392 time to fit residues: 83.3740 Evaluate side-chains 85 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 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 240 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7692 Z= 0.221 Angle : 0.607 7.670 10484 Z= 0.297 Chirality : 0.040 0.198 1244 Planarity : 0.004 0.045 1266 Dihedral : 7.142 47.057 1328 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.52 % Favored : 95.27 % Rotamer: Outliers : 3.06 % Allowed : 15.56 % Favored : 81.38 % 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: 1.71 (0.28), residues: 952 helix: 2.02 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -1.57 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 197 HIS 0.002 0.001 HIS B 362 PHE 0.013 0.001 PHE A 194 TYR 0.008 0.001 TYR A 335 ARG 0.002 0.000 ARG A 404 *********************** 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 108 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.8494 (mmm) cc_final: 0.8112 (tpt) REVERT: B 340 THR cc_start: 0.8896 (m) cc_final: 0.8606 (m) REVERT: B 413 MET cc_start: 0.8559 (ttp) cc_final: 0.8240 (ttp) REVERT: A 340 THR cc_start: 0.8883 (m) cc_final: 0.8588 (m) REVERT: A 413 MET cc_start: 0.8541 (ttp) cc_final: 0.8217 (ttp) outliers start: 23 outliers final: 14 residues processed: 91 average time/residue: 0.7805 time to fit residues: 77.7155 Evaluate side-chains 96 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 484 MET 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 240 PHE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 484 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.0470 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 23 optimal weight: 0.0000 chunk 31 optimal weight: 0.6980 overall best weight: 0.3482 ------------------------------------------------------------------------------- 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 ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7692 Z= 0.169 Angle : 0.562 7.664 10484 Z= 0.275 Chirality : 0.037 0.172 1244 Planarity : 0.004 0.036 1266 Dihedral : 6.520 40.465 1328 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.20 % Favored : 95.59 % Rotamer: Outliers : 2.66 % Allowed : 16.89 % Favored : 80.45 % 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: 2.02 (0.29), residues: 952 helix: 2.26 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.54 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.001 0.000 HIS A 348 PHE 0.010 0.001 PHE A 194 TYR 0.007 0.001 TYR A 113 ARG 0.002 0.000 ARG A 404 *********************** 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 112 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.8253 (mmm) cc_final: 0.7963 (mmm) REVERT: B 340 THR cc_start: 0.8811 (m) cc_final: 0.8529 (m) REVERT: B 413 MET cc_start: 0.8589 (ttp) cc_final: 0.8261 (ttp) REVERT: A 340 THR cc_start: 0.8816 (m) cc_final: 0.8521 (m) REVERT: A 413 MET cc_start: 0.8574 (ttp) cc_final: 0.8240 (ttp) outliers start: 20 outliers final: 9 residues processed: 97 average time/residue: 0.8098 time to fit residues: 85.3891 Evaluate side-chains 96 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 371 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.003 0.037 7692 Z= 0.207 Angle : 0.583 8.535 10484 Z= 0.285 Chirality : 0.038 0.130 1244 Planarity : 0.004 0.035 1266 Dihedral : 6.488 39.222 1328 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.10 % Favored : 95.69 % 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: 1.98 (0.28), residues: 952 helix: 2.22 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -1.50 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 113 ARG 0.001 0.000 ARG A 129 *********************** 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 104 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 80 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 THR cc_start: 0.8847 (m) cc_final: 0.8541 (m) REVERT: B 413 MET cc_start: 0.8614 (ttp) cc_final: 0.8303 (ttp) REVERT: A 340 THR cc_start: 0.8844 (m) cc_final: 0.8535 (m) REVERT: A 413 MET cc_start: 0.8598 (ttp) cc_final: 0.8289 (ttp) outliers start: 24 outliers final: 14 residues processed: 95 average time/residue: 0.7946 time to fit residues: 82.2467 Evaluate side-chains 87 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 464 SER Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 484 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 0.2980 chunk 57 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7692 Z= 0.193 Angle : 0.570 7.047 10484 Z= 0.280 Chirality : 0.038 0.130 1244 Planarity : 0.003 0.035 1266 Dihedral : 6.342 43.405 1328 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.41 % Favored : 95.38 % Rotamer: Outliers : 3.72 % Allowed : 16.62 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.02 (0.28), residues: 952 helix: 2.25 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.49 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 453 HIS 0.002 0.001 HIS A 348 PHE 0.012 0.001 PHE A 194 TYR 0.009 0.001 TYR A 113 ARG 0.001 0.000 ARG A 129 *********************** 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 99 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 71 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 301 MET cc_start: 0.5387 (OUTLIER) cc_final: 0.4858 (mmt) REVERT: B 340 THR cc_start: 0.8833 (m) cc_final: 0.8549 (m) REVERT: B 413 MET cc_start: 0.8621 (ttp) cc_final: 0.8308 (ttp) REVERT: A 301 MET cc_start: 0.5380 (OUTLIER) cc_final: 0.4792 (mmt) REVERT: A 340 THR cc_start: 0.8838 (m) cc_final: 0.8545 (m) REVERT: A 413 MET cc_start: 0.8570 (ttp) cc_final: 0.8250 (ttp) outliers start: 28 outliers final: 10 residues processed: 87 average time/residue: 0.8609 time to fit residues: 81.1229 Evaluate side-chains 78 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 301 MET Chi-restraints excluded: chain B residue 464 SER 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 301 MET 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 27 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 58 optimal weight: 0.0870 chunk 63 optimal weight: 0.0270 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 84 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 GLN A 457 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7692 Z= 0.159 Angle : 0.535 6.847 10484 Z= 0.264 Chirality : 0.036 0.126 1244 Planarity : 0.003 0.034 1266 Dihedral : 5.987 48.288 1328 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.10 % Favored : 95.69 % Rotamer: Outliers : 2.66 % Allowed : 17.69 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.01 (0.28), residues: 952 helix: 2.28 (0.20), residues: 714 sheet: None (None), residues: 0 loop : -1.77 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 197 HIS 0.001 0.000 HIS B 348 PHE 0.010 0.001 PHE A 194 TYR 0.009 0.001 TYR A 113 ARG 0.001 0.000 ARG B 129 *********************** 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 96 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 THR cc_start: 0.8775 (m) cc_final: 0.8493 (m) REVERT: B 413 MET cc_start: 0.8598 (ttp) cc_final: 0.8320 (ttp) REVERT: A 340 THR cc_start: 0.8779 (m) cc_final: 0.8489 (m) REVERT: A 413 MET cc_start: 0.8558 (ttp) cc_final: 0.8275 (ttp) outliers start: 20 outliers final: 9 residues processed: 88 average time/residue: 0.8224 time to fit residues: 78.8229 Evaluate side-chains 82 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 464 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 176 THR Chi-restraints excluded: chain A residue 207 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 86 optimal weight: 0.0020 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 77 optimal weight: 0.0870 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 overall best weight: 0.4966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 GLN A 457 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7692 Z= 0.172 Angle : 0.542 7.191 10484 Z= 0.266 Chirality : 0.037 0.128 1244 Planarity : 0.003 0.033 1266 Dihedral : 5.938 50.807 1328 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.99 % Allowed : 18.88 % 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: 1.95 (0.28), residues: 952 helix: 2.22 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -1.77 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.002 0.001 HIS B 348 PHE 0.011 0.001 PHE A 194 TYR 0.008 0.001 TYR A 113 ARG 0.001 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.7663 (mmm) cc_final: 0.7400 (mmm) REVERT: B 340 THR cc_start: 0.8814 (m) cc_final: 0.8526 (m) REVERT: B 413 MET cc_start: 0.8607 (ttp) cc_final: 0.8290 (ttp) REVERT: A 340 THR cc_start: 0.8818 (m) cc_final: 0.8516 (m) REVERT: A 413 MET cc_start: 0.8561 (ttp) cc_final: 0.8251 (ttp) outliers start: 15 outliers final: 12 residues processed: 88 average time/residue: 0.8992 time to fit residues: 86.0405 Evaluate side-chains 87 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain B residue 207 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 118 LEU Chi-restraints excluded: chain A residue 176 THR 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 55 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7692 Z= 0.224 Angle : 0.588 7.291 10484 Z= 0.287 Chirality : 0.039 0.132 1244 Planarity : 0.003 0.034 1266 Dihedral : 6.216 53.417 1328 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.26 % Allowed : 18.62 % 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: 1.92 (0.28), residues: 952 helix: 2.17 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.53 (0.40), 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 0.013 0.001 PHE A 194 TYR 0.010 0.001 TYR A 113 ARG 0.002 0.000 ARG B 350 ********************** 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 87 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.8072 (mmm) cc_final: 0.7773 (mmm) REVERT: B 340 THR cc_start: 0.8884 (m) cc_final: 0.8567 (m) REVERT: B 413 MET cc_start: 0.8643 (ttp) cc_final: 0.8305 (ttp) REVERT: A 340 THR cc_start: 0.8877 (m) cc_final: 0.8556 (m) REVERT: A 413 MET cc_start: 0.8620 (ttp) cc_final: 0.8295 (ttp) outliers start: 17 outliers final: 10 residues processed: 79 average time/residue: 0.8828 time to fit residues: 76.1669 Evaluate side-chains 80 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 207 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 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 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.0670 chunk 11 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106000 restraints weight = 9050.950| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.55 r_work: 0.2968 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7692 Z= 0.184 Angle : 0.555 7.033 10484 Z= 0.272 Chirality : 0.038 0.130 1244 Planarity : 0.003 0.033 1266 Dihedral : 6.119 57.416 1328 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.73 % Allowed : 19.55 % Favored : 78.72 % 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: 1.81 (0.28), residues: 952 helix: 2.13 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -1.85 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 453 HIS 0.002 0.001 HIS B 348 PHE 0.012 0.001 PHE A 194 TYR 0.010 0.001 TYR A 113 ARG 0.001 0.000 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2480.45 seconds wall clock time: 44 minutes 29.30 seconds (2669.30 seconds total)