Starting phenix.real_space_refine on Fri Dec 8 06:42:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzs_36752/12_2023/8jzs_36752_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzs_36752/12_2023/8jzs_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_36752/12_2023/8jzs_36752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzs_36752/12_2023/8jzs_36752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzs_36752/12_2023/8jzs_36752_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzs_36752/12_2023/8jzs_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-1.21rc1-5172/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: 4.57, 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: 2.91 Conformation dependent library (CDL) restraints added in 1.3 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: 1.41 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: 1.92 Time building geometry restraints manager: 3.17 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: 0.700 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: 3.310 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.430 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:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.490 ------------------------------------------------------------------------------- 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 : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.6849 time to fit residues: 111.8306 Evaluate side-chains 90 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.758 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0301 ------------------------------------------------------------------------------- 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: 0.8179 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7692 Z= 0.298 Angle : 0.685 7.681 10484 Z= 0.336 Chirality : 0.042 0.156 1244 Planarity : 0.006 0.075 1266 Dihedral : 8.446 53.502 1328 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.62 % Favored : 95.17 % Rotamer: Outliers : 2.39 % Allowed : 10.90 % Favored : 86.70 % 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: 0.62 (0.28), residues: 952 helix: 1.22 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -1.75 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 453 HIS 0.006 0.001 HIS A 362 PHE 0.033 0.002 PHE A 240 TYR 0.017 0.002 TYR A 113 ARG 0.003 0.001 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 116 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 104 average time/residue: 0.7450 time to fit residues: 84.8571 Evaluate side-chains 90 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 5 average time/residue: 0.1440 time to fit residues: 2.0234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 72 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 87 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8196 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7692 Z= 0.239 Angle : 0.614 8.114 10484 Z= 0.299 Chirality : 0.039 0.134 1244 Planarity : 0.005 0.071 1266 Dihedral : 7.191 47.898 1328 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.31 % Favored : 95.48 % Rotamer: Outliers : 4.65 % Allowed : 13.03 % Favored : 82.31 % 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: 0.96 (0.28), residues: 952 helix: 1.50 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -1.69 (0.39), residues: 264 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 0.012 0.001 PHE B 194 TYR 0.009 0.001 TYR B 335 ARG 0.002 0.000 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 110 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 75 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 16 residues processed: 91 average time/residue: 0.8341 time to fit residues: 82.7913 Evaluate side-chains 86 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 0.834 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 0.5135 time to fit residues: 4.0092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8182 moved from start: 0.2902 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= 0.201 Angle : 0.578 7.645 10484 Z= 0.281 Chirality : 0.038 0.130 1244 Planarity : 0.005 0.071 1266 Dihedral : 6.850 42.952 1328 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.20 % Favored : 95.59 % Rotamer: Outliers : 3.86 % Allowed : 14.89 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.28), residues: 952 helix: 1.65 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -1.77 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 197 HIS 0.002 0.001 HIS B 348 PHE 0.012 0.001 PHE A 194 TYR 0.008 0.001 TYR A 335 ARG 0.001 0.000 ARG B 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 110 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 81 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 94 average time/residue: 0.8460 time to fit residues: 86.5961 Evaluate side-chains 90 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.1150 time to fit residues: 1.6249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.0770 chunk 1 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 79 optimal weight: 0.0870 chunk 64 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 overall best weight: 0.4516 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8154 moved from start: 0.2987 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= 0.175 Angle : 0.541 5.758 10484 Z= 0.267 Chirality : 0.037 0.126 1244 Planarity : 0.005 0.069 1266 Dihedral : 6.365 38.890 1328 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.99 % Favored : 95.80 % Rotamer: Outliers : 3.59 % Allowed : 15.96 % 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: 1.26 (0.28), residues: 952 helix: 1.74 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -1.71 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.002 0.000 HIS B 348 PHE 0.011 0.001 PHE A 194 TYR 0.009 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 110 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 95 average time/residue: 0.7600 time to fit residues: 79.2243 Evaluate side-chains 90 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.8056 time to fit residues: 3.6919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.8980 chunk 18 optimal weight: 0.0370 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 89 optimal weight: 0.0050 overall best weight: 0.4672 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8154 moved from start: 0.3108 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= 0.174 Angle : 0.543 5.782 10484 Z= 0.266 Chirality : 0.037 0.123 1244 Planarity : 0.005 0.068 1266 Dihedral : 6.181 42.663 1328 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.89 % Favored : 95.90 % Rotamer: Outliers : 3.59 % Allowed : 16.36 % 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: 1.24 (0.28), residues: 952 helix: 1.73 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -1.75 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 453 HIS 0.001 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 404 *********************** 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 108 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 81 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 92 average time/residue: 0.8306 time to fit residues: 83.3240 Evaluate side-chains 86 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.721 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.1130 time to fit residues: 1.1577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 0.0980 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 0.0030 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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: 0.8153 moved from start: 0.3176 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= 0.177 Angle : 0.545 6.912 10484 Z= 0.266 Chirality : 0.036 0.122 1244 Planarity : 0.005 0.073 1266 Dihedral : 6.056 46.723 1328 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.53 % Allowed : 18.35 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.28), residues: 952 helix: 1.77 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -1.71 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 453 HIS 0.002 0.001 HIS B 348 PHE 0.010 0.001 PHE B 194 TYR 0.010 0.001 TYR B 113 ARG 0.001 0.000 ARG A 404 *********************** 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 93 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 85 average time/residue: 0.8287 time to fit residues: 76.8993 Evaluate side-chains 88 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 0.4960 time to fit residues: 3.8430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.5052 > 50: distance: 1 - 26: 31.777 distance: 5 - 34: 27.384 distance: 23 - 26: 35.102 distance: 26 - 27: 24.112 distance: 27 - 28: 38.655 distance: 27 - 30: 27.036 distance: 28 - 29: 24.738 distance: 28 - 34: 17.331 distance: 30 - 31: 15.303 distance: 31 - 32: 13.262 distance: 31 - 33: 15.846 distance: 34 - 35: 12.999 distance: 35 - 36: 17.041 distance: 35 - 38: 28.547 distance: 36 - 37: 6.992 distance: 36 - 39: 27.032 distance: 39 - 40: 31.971 distance: 40 - 41: 28.644 distance: 40 - 43: 23.886 distance: 41 - 42: 13.212 distance: 41 - 50: 9.286 distance: 43 - 44: 22.138 distance: 44 - 45: 32.541 distance: 45 - 46: 36.607 distance: 46 - 47: 25.589 distance: 47 - 48: 30.064 distance: 47 - 49: 10.816 distance: 50 - 51: 3.686 distance: 51 - 52: 19.469 distance: 51 - 54: 17.779 distance: 52 - 53: 17.840 distance: 52 - 58: 15.832 distance: 54 - 55: 33.039 distance: 55 - 56: 21.560 distance: 55 - 57: 37.413 distance: 58 - 59: 3.704 distance: 59 - 60: 21.900 distance: 60 - 61: 17.029 distance: 60 - 62: 32.079 distance: 62 - 63: 11.839 distance: 63 - 64: 14.765 distance: 63 - 66: 10.005 distance: 64 - 65: 23.794 distance: 64 - 73: 15.718 distance: 65 - 94: 26.298 distance: 66 - 67: 33.133 distance: 67 - 68: 43.702 distance: 68 - 69: 10.593 distance: 69 - 70: 18.021 distance: 70 - 71: 16.374 distance: 70 - 72: 9.579 distance: 73 - 74: 10.325 distance: 74 - 75: 10.221 distance: 74 - 77: 21.892 distance: 75 - 78: 13.550 distance: 76 - 102: 19.412 distance: 78 - 79: 12.938 distance: 79 - 80: 19.662 distance: 79 - 82: 20.985 distance: 80 - 81: 9.961 distance: 80 - 89: 4.862 distance: 81 - 110: 22.282 distance: 82 - 83: 28.488 distance: 83 - 84: 35.387 distance: 84 - 85: 41.031 distance: 85 - 86: 21.127 distance: 86 - 87: 12.807 distance: 86 - 88: 25.765 distance: 89 - 90: 42.796 distance: 90 - 91: 20.003 distance: 90 - 93: 18.910 distance: 91 - 94: 9.010 distance: 92 - 117: 30.705 distance: 94 - 95: 3.593 distance: 95 - 96: 14.939 distance: 95 - 98: 8.550 distance: 96 - 97: 6.651 distance: 96 - 102: 23.137 distance: 97 - 123: 25.527 distance: 98 - 99: 3.054 distance: 98 - 100: 16.942 distance: 99 - 101: 30.233