Starting phenix.real_space_refine on Sat Apr 6 07:04:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzs_36752/04_2024/8jzs_36752_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzs_36752/04_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_36752/04_2024/8jzs_36752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzs_36752/04_2024/8jzs_36752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzs_36752/04_2024/8jzs_36752_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzs_36752/04_2024/8jzs_36752_updated.pdb" } 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-5288/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: 4.55, per 1000 atoms: 0.61 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: 2.90 Conformation dependent library (CDL) restraints added in 1.4 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... running ksdssp... Secondary structure from input PDB file: 36 helices and 2 sheets defined 73.7% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'B' and resid 19 through 27 Processing helix chain 'B' and resid 35 through 56 removed outlier: 3.801A pdb=" N VAL B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 71 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 102 through 124 removed outlier: 4.002A pdb=" N ALA B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 126 through 133 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 154 through 183 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 187 through 211 removed outlier: 4.269A pdb=" N THR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 219 removed outlier: 3.631A pdb=" N GLN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 242 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 261 Processing helix chain 'B' and resid 311 through 348 Proline residue: B 323 - end of helix removed outlier: 3.878A pdb=" N ILE B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) Proline residue: B 330 - end of helix 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: 3.961A pdb=" N LEU B 378 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Proline residue: B 382 - end of helix Processing helix chain 'B' and resid 391 through 394 No H-bonds generated for 'chain 'B' and resid 391 through 394' Processing helix chain 'B' and resid 401 through 430 removed outlier: 3.782A pdb=" N ILE B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 478 Proline residue: B 456 - end of helix removed outlier: 3.850A pdb=" N LEU B 459 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE B 461 " --> pdb=" O TYR B 458 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 463 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA B 468 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N SER B 469 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 470 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 472 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 478 " --> pdb=" O PHE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 509 Processing helix chain 'B' and resid 532 through 557 Processing helix chain 'A' and resid 19 through 27 Processing helix chain 'A' and resid 35 through 56 removed outlier: 3.801A pdb=" N VAL A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 71 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 102 through 124 removed outlier: 4.002A pdb=" N ALA A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 126 through 133 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 154 through 183 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 187 through 211 removed outlier: 4.269A pdb=" N THR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 219 removed outlier: 3.631A pdb=" N GLN A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 242 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 261 Processing helix chain 'A' and resid 311 through 348 Proline residue: A 323 - end of helix removed outlier: 3.878A pdb=" N ILE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Proline residue: A 330 - end of helix 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: 3.961A pdb=" N LEU A 378 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Proline residue: A 382 - end of helix Processing helix chain 'A' and resid 391 through 394 No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 401 through 430 removed outlier: 3.782A pdb=" N ILE A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 478 Proline residue: A 456 - end of helix removed outlier: 3.850A pdb=" N LEU A 459 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 461 " --> pdb=" O TYR A 458 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 463 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA A 468 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N SER A 469 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 470 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 471 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 472 " --> pdb=" O SER A 469 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 478 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 509 Processing helix chain 'A' and resid 532 through 557 Processing sheet with id= A, first strand: chain 'B' and resid 435 through 439 removed outlier: 3.655A pdb=" N VAL B 442 " --> pdb=" O ILE B 439 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 435 through 439 removed outlier: 3.655A pdb=" N VAL A 442 " --> pdb=" O ILE A 439 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 3.15 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: 2259 2.82 - 3.34: 7556 3.34 - 3.86: 12324 3.86 - 4.38: 14490 4.38 - 4.90: 24745 Nonbonded interactions: 61374 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 61369 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.390 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.900 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 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:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.430 ------------------------------------------------------------------------------- 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= 0.505 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 : 0.796 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: 0.7319 time to fit residues: 119.2981 Evaluate side-chains 90 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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: 0.9990 chunk 72 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 A 57 ASN A 63 ASN A 196 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7692 Z= 0.297 Angle : 0.679 8.126 10484 Z= 0.332 Chirality : 0.041 0.152 1244 Planarity : 0.005 0.075 1266 Dihedral : 8.403 53.728 1328 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.41 % Favored : 95.38 % Rotamer: Outliers : 2.39 % Allowed : 10.37 % Favored : 87.23 % 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: 0.67 (0.28), residues: 952 helix: 1.26 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -1.73 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 453 HIS 0.004 0.001 HIS A 362 PHE 0.031 0.002 PHE A 240 TYR 0.017 0.002 TYR B 113 ARG 0.003 0.000 ARG A 186 *********************** 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 fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.8445 (mmm) cc_final: 0.8170 (tpt) REVERT: B 340 THR cc_start: 0.8942 (m) cc_final: 0.8637 (m) REVERT: B 413 MET cc_start: 0.8650 (ttp) cc_final: 0.8343 (ttp) REVERT: A 117 MET cc_start: 0.8475 (mmm) cc_final: 0.8248 (tpt) REVERT: A 340 THR cc_start: 0.8936 (m) cc_final: 0.8624 (m) REVERT: A 413 MET cc_start: 0.8632 (ttp) cc_final: 0.8296 (ttp) outliers start: 18 outliers final: 10 residues processed: 101 average time/residue: 0.7876 time to fit residues: 87.0793 Evaluate side-chains 92 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 511 SER Chi-restraints excluded: chain B residue 526 ASN 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 511 SER Chi-restraints excluded: chain A residue 526 ASN 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: 8.9990 chunk 24 optimal weight: 9.9990 chunk 87 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 0.0020 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN B 457 GLN A 63 ASN A 457 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7692 Z= 0.219 Angle : 0.610 7.319 10484 Z= 0.295 Chirality : 0.039 0.134 1244 Planarity : 0.005 0.072 1266 Dihedral : 7.400 50.027 1328 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.57 % Favored : 96.22 % Rotamer: Outliers : 3.59 % Allowed : 12.23 % 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: 0.94 (0.28), residues: 952 helix: 1.48 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -1.72 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 197 HIS 0.002 0.001 HIS B 348 PHE 0.012 0.001 PHE A 194 TYR 0.011 0.001 TYR A 113 ARG 0.002 0.000 ARG B 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 111 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 84 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 THR cc_start: 0.8903 (m) cc_final: 0.8610 (m) REVERT: B 413 MET cc_start: 0.8618 (ttp) cc_final: 0.8298 (ttp) REVERT: A 340 THR cc_start: 0.8892 (m) cc_final: 0.8593 (m) REVERT: A 413 MET cc_start: 0.8600 (ttp) cc_final: 0.8281 (ttp) outliers start: 27 outliers final: 15 residues processed: 97 average time/residue: 0.8607 time to fit residues: 90.6333 Evaluate side-chains 93 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 483 SER Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 526 ASN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 511 SER 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 86 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.0020 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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: 0.8176 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7692 Z= 0.204 Angle : 0.577 7.786 10484 Z= 0.282 Chirality : 0.038 0.127 1244 Planarity : 0.005 0.071 1266 Dihedral : 6.886 44.413 1328 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.99 % Favored : 95.80 % Rotamer: Outliers : 3.46 % Allowed : 14.89 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 952 helix: 1.66 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -1.73 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 197 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 0.002 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 109 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 83 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 THR cc_start: 0.8865 (m) cc_final: 0.8589 (m) REVERT: B 413 MET cc_start: 0.8625 (ttp) cc_final: 0.8318 (ttp) REVERT: A 340 THR cc_start: 0.8859 (m) cc_final: 0.8574 (m) REVERT: A 413 MET cc_start: 0.8602 (ttp) cc_final: 0.8301 (ttp) outliers start: 26 outliers final: 12 residues processed: 94 average time/residue: 0.7936 time to fit residues: 81.5804 Evaluate side-chains 90 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 240 PHE Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 526 ASN 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 Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 526 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 0.0050 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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: 0.8168 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7692 Z= 0.186 Angle : 0.562 8.010 10484 Z= 0.276 Chirality : 0.037 0.125 1244 Planarity : 0.005 0.070 1266 Dihedral : 6.647 41.616 1328 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.78 % Favored : 96.01 % Rotamer: Outliers : 2.93 % Allowed : 16.36 % 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: 1.19 (0.28), residues: 952 helix: 1.68 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -1.68 (0.39), residues: 262 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 0.008 0.001 TYR A 335 ARG 0.001 0.000 ARG B 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 106 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 THR cc_start: 0.8840 (m) cc_final: 0.8576 (m) REVERT: B 413 MET cc_start: 0.8627 (ttp) cc_final: 0.8344 (ttp) REVERT: A 340 THR cc_start: 0.8840 (m) cc_final: 0.8570 (m) REVERT: A 413 MET cc_start: 0.8602 (ttp) cc_final: 0.8330 (ttp) outliers start: 22 outliers final: 12 residues processed: 95 average time/residue: 0.8411 time to fit residues: 86.9883 Evaluate side-chains 92 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 483 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 526 ASN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 526 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 0.0020 chunk 92 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 0.0010 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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: 0.8152 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7692 Z= 0.178 Angle : 0.553 6.898 10484 Z= 0.270 Chirality : 0.037 0.123 1244 Planarity : 0.005 0.069 1266 Dihedral : 6.304 39.743 1328 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.68 % Favored : 96.11 % Rotamer: Outliers : 3.46 % Allowed : 16.22 % 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: 1.22 (0.28), residues: 952 helix: 1.71 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -1.71 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 PHE 0.011 0.001 PHE A 194 TYR 0.010 0.001 TYR A 113 ARG 0.001 0.000 ARG A 102 *********************** 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 107 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 THR cc_start: 0.8818 (m) cc_final: 0.8550 (m) REVERT: B 413 MET cc_start: 0.8644 (ttp) cc_final: 0.8348 (ttp) REVERT: A 340 THR cc_start: 0.8826 (m) cc_final: 0.8549 (m) REVERT: A 413 MET cc_start: 0.8622 (ttp) cc_final: 0.8335 (ttp) outliers start: 26 outliers final: 12 residues processed: 94 average time/residue: 0.7493 time to fit residues: 77.5257 Evaluate side-chains 86 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 240 PHE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 511 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 Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 511 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 0.0000 chunk 67 optimal weight: 0.0670 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 0.1980 overall best weight: 0.2922 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7692 Z= 0.162 Angle : 0.540 7.608 10484 Z= 0.262 Chirality : 0.036 0.123 1244 Planarity : 0.004 0.067 1266 Dihedral : 5.939 44.548 1328 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.99 % Favored : 95.80 % Rotamer: Outliers : 2.79 % Allowed : 17.15 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.29), residues: 952 helix: 1.77 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -1.72 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 197 HIS 0.001 0.000 HIS A 348 PHE 0.009 0.001 PHE A 194 TYR 0.010 0.001 TYR A 113 ARG 0.001 0.000 ARG B 102 *********************** 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 104 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 THR cc_start: 0.8759 (m) cc_final: 0.8496 (m) REVERT: B 413 MET cc_start: 0.8648 (ttp) cc_final: 0.8372 (ttp) REVERT: A 172 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8695 (mtmt) REVERT: A 340 THR cc_start: 0.8764 (m) cc_final: 0.8508 (m) REVERT: A 413 MET cc_start: 0.8627 (ttp) cc_final: 0.8360 (ttp) outliers start: 21 outliers final: 13 residues processed: 93 average time/residue: 0.8089 time to fit residues: 82.1340 Evaluate side-chains 92 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 240 PHE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 526 ASN 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 172 LYS Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 511 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 80 optimal weight: 0.0020 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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: 0.8150 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7692 Z= 0.180 Angle : 0.542 5.963 10484 Z= 0.266 Chirality : 0.037 0.122 1244 Planarity : 0.005 0.073 1266 Dihedral : 5.942 47.826 1328 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.32 % Allowed : 17.02 % 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: 1.33 (0.29), residues: 952 helix: 1.80 (0.21), residues: 690 sheet: None (None), residues: 0 loop : -1.71 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 453 HIS 0.002 0.001 HIS B 348 PHE 0.010 0.001 PHE B 194 TYR 0.009 0.001 TYR B 113 ARG 0.001 0.000 ARG B 350 *********************** 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 100 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 75 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 THR cc_start: 0.8834 (m) cc_final: 0.8557 (m) REVERT: B 413 MET cc_start: 0.8652 (ttp) cc_final: 0.8352 (ttp) REVERT: A 172 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8676 (mtmt) REVERT: A 340 THR cc_start: 0.8819 (m) cc_final: 0.8549 (m) REVERT: A 413 MET cc_start: 0.8587 (ttp) cc_final: 0.8283 (ttp) outliers start: 25 outliers final: 17 residues processed: 89 average time/residue: 0.8395 time to fit residues: 81.4965 Evaluate side-chains 92 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 240 PHE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 526 ASN 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 172 LYS Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 526 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3197 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= 0.178 Angle : 0.534 6.403 10484 Z= 0.262 Chirality : 0.037 0.122 1244 Planarity : 0.005 0.074 1266 Dihedral : 5.940 51.368 1328 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.53 % Allowed : 17.95 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.28), residues: 952 helix: 1.81 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -1.74 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 *********************** 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 98 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 THR cc_start: 0.8847 (m) cc_final: 0.8547 (m) REVERT: B 413 MET cc_start: 0.8587 (ttp) cc_final: 0.8284 (ttp) REVERT: A 172 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8669 (mtmt) REVERT: A 340 THR cc_start: 0.8833 (m) cc_final: 0.8541 (m) REVERT: A 413 MET cc_start: 0.8568 (ttp) cc_final: 0.8273 (ttp) outliers start: 19 outliers final: 16 residues processed: 90 average time/residue: 0.8088 time to fit residues: 79.4372 Evaluate side-chains 93 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 240 PHE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 526 ASN 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 172 LYS Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 526 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.0000 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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: 0.8176 moved from start: 0.3268 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= 0.200 Angle : 0.554 5.991 10484 Z= 0.272 Chirality : 0.038 0.125 1244 Planarity : 0.005 0.074 1266 Dihedral : 6.012 54.458 1328 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.32 % Allowed : 17.55 % 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: 1.26 (0.28), residues: 952 helix: 1.77 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -1.79 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 404 ********************** 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 102 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 THR cc_start: 0.8874 (m) cc_final: 0.8582 (m) REVERT: B 413 MET cc_start: 0.8602 (ttp) cc_final: 0.8276 (ttp) REVERT: A 172 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8691 (mtmt) REVERT: A 340 THR cc_start: 0.8863 (m) cc_final: 0.8564 (m) REVERT: A 413 MET cc_start: 0.8580 (ttp) cc_final: 0.8257 (ttp) outliers start: 25 outliers final: 12 residues processed: 91 average time/residue: 0.8311 time to fit residues: 82.8286 Evaluate side-chains 90 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 511 SER Chi-restraints excluded: chain B residue 526 ASN 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 172 LYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 526 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.0370 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.134248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.101032 restraints weight = 9325.467| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.71 r_work: 0.2992 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 0.034 7692 Z= 0.173 Angle : 0.540 7.151 10484 Z= 0.264 Chirality : 0.037 0.123 1244 Planarity : 0.005 0.074 1266 Dihedral : 5.918 57.821 1328 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.13 % Allowed : 19.02 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.31 (0.28), residues: 952 helix: 1.82 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -1.81 (0.37), residues: 262 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 0.010 0.001 PHE B 194 TYR 0.008 0.001 TYR B 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: 2506.05 seconds wall clock time: 45 minutes 43.59 seconds (2743.59 seconds total)