Starting phenix.real_space_refine on Thu Jul 2 09:43:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z29_14458/07_2026/7z29_14458.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z29_14458/07_2026/7z29_14458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7z29_14458/07_2026/7z29_14458.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z29_14458/07_2026/7z29_14458.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z29_14458/07_2026/7z29_14458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z29_14458/07_2026/7z29_14458.map" model { file = "/net/cci-nas-00/data/ceres_data/7z29_14458/07_2026/7z29_14458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z29_14458/07_2026/7z29_14458.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.022 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: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 12 5.16 5 C 5264 2.51 5 N 1388 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8307 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4268 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 494} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3298 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 30, 'TRANS': 374} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 721 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'NVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.40, per 1000 atoms: 0.17 Number of scatterers: 8307 At special positions: 0 Unit cell: (98.94, 109.61, 95.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 35 15.00 O 1608 8.00 N 1388 7.00 C 5264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 278.8 milliseconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 38.8% alpha, 15.2% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 removed outlier: 3.892A pdb=" N LEU A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.969A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.516A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 296 through 311 Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 404 removed outlier: 3.734A pdb=" N GLU A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 4.220A pdb=" N ILE A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.604A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.740A pdb=" N ASN A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.713A pdb=" N VAL A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 549 " --> pdb=" O ASN A 545 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 4.121A pdb=" N LEU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 89 removed outlier: 5.543A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.527A pdb=" N LYS B 101 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 102 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 103 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.852A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.641A pdb=" N ASN B 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 138 " --> pdb=" O ILE B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 134 through 138' Processing helix chain 'B' and resid 154 through 175 removed outlier: 4.081A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.802A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.525A pdb=" N TRP B 239 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 271 removed outlier: 4.186A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE B 270 " --> pdb=" O TRP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.568A pdb=" N TRP B 406 " --> pdb=" O THR B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 354 removed outlier: 7.228A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS A 353 " --> pdb=" O TRP A 337 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP A 337 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 340 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 328 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 390 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.706A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 464 through 470 removed outlier: 3.968A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 493 " --> pdb=" O LYS A 530 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AA8, first strand: chain 'B' and resid 61 through 64 Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 183 removed outlier: 3.582A pdb=" N SER B 191 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 252 through 253 removed outlier: 4.305A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.139A pdb=" N GLU B 344 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 339 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.139A pdb=" N GLU B 344 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA B 327 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1309 1.31 - 1.44: 2388 1.44 - 1.56: 4808 1.56 - 1.68: 69 1.68 - 1.81: 21 Bond restraints: 8595 Sorted by residual: bond pdb=" C4' DG E 19 " pdb=" O4' DG E 19 " ideal model delta sigma weight residual 1.446 1.515 -0.069 1.00e-02 1.00e+04 4.82e+01 bond pdb=" C4' DA E 26 " pdb=" O4' DA E 26 " ideal model delta sigma weight residual 1.446 1.405 0.041 1.00e-02 1.00e+04 1.65e+01 bond pdb=" CA LYS B 138 " pdb=" C LYS B 138 " ideal model delta sigma weight residual 1.523 1.472 0.052 1.30e-02 5.92e+03 1.58e+01 bond pdb=" N ILE B 132 " pdb=" CA ILE B 132 " ideal model delta sigma weight residual 1.460 1.489 -0.029 7.50e-03 1.78e+04 1.52e+01 bond pdb=" CA LEU A 260 " pdb=" C LEU A 260 " ideal model delta sigma weight residual 1.524 1.481 0.042 1.26e-02 6.30e+03 1.13e+01 ... (remaining 8590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 11648 2.85 - 5.70: 175 5.70 - 8.55: 18 8.55 - 11.40: 1 11.40 - 14.25: 2 Bond angle restraints: 11844 Sorted by residual: angle pdb=" N PRO A 412 " pdb=" CA PRO A 412 " pdb=" C PRO A 412 " ideal model delta sigma weight residual 112.47 126.72 -14.25 2.06e+00 2.36e-01 4.79e+01 angle pdb=" C5' DG E 19 " pdb=" C4' DG E 19 " pdb=" O4' DG E 19 " ideal model delta sigma weight residual 109.30 121.13 -11.83 1.90e+00 2.77e-01 3.88e+01 angle pdb=" O4' DC E 3 " pdb=" C4' DC E 3 " pdb=" C3' DC E 3 " ideal model delta sigma weight residual 106.00 102.63 3.37 6.00e-01 2.78e+00 3.15e+01 angle pdb=" C5' DC E 3 " pdb=" C4' DC E 3 " pdb=" O4' DC E 3 " ideal model delta sigma weight residual 109.30 119.40 -10.10 1.90e+00 2.77e-01 2.83e+01 angle pdb=" CA GLY B 333 " pdb=" C GLY B 333 " pdb=" O GLY B 333 " ideal model delta sigma weight residual 122.24 117.62 4.62 8.70e-01 1.32e+00 2.82e+01 ... (remaining 11839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4309 17.69 - 35.38: 542 35.38 - 53.07: 126 53.07 - 70.76: 41 70.76 - 88.46: 6 Dihedral angle restraints: 5024 sinusoidal: 2291 harmonic: 2733 Sorted by residual: dihedral pdb=" C TYR A 183 " pdb=" N TYR A 183 " pdb=" CA TYR A 183 " pdb=" CB TYR A 183 " ideal model delta harmonic sigma weight residual -122.60 -111.33 -11.27 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" C LYS B 424 " pdb=" N LYS B 424 " pdb=" CA LYS B 424 " pdb=" CB LYS B 424 " ideal model delta harmonic sigma weight residual -122.60 -133.72 11.12 0 2.50e+00 1.60e-01 1.98e+01 dihedral pdb=" CA GLU B 44 " pdb=" C GLU B 44 " pdb=" N GLY B 45 " pdb=" CA GLY B 45 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 5021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1102 0.074 - 0.148: 157 0.148 - 0.222: 28 0.222 - 0.297: 10 0.297 - 0.371: 7 Chirality restraints: 1304 Sorted by residual: chirality pdb=" CA GLU B 415 " pdb=" N GLU B 415 " pdb=" C GLU B 415 " pdb=" CB GLU B 415 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA TYR A 183 " pdb=" N TYR A 183 " pdb=" C TYR A 183 " pdb=" CB TYR A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA LYS B 101 " pdb=" N LYS B 101 " pdb=" C LYS B 101 " pdb=" CB LYS B 101 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 1301 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 307 " 0.465 9.50e-02 1.11e+02 2.09e-01 2.66e+01 pdb=" NE ARG A 307 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 307 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 307 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 307 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 156 " 0.059 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO B 157 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 130 " 0.018 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C PHE B 130 " -0.060 2.00e-02 2.50e+03 pdb=" O PHE B 130 " 0.022 2.00e-02 2.50e+03 pdb=" N THR B 131 " 0.020 2.00e-02 2.50e+03 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2406 2.82 - 3.34: 7260 3.34 - 3.86: 13458 3.86 - 4.38: 15856 4.38 - 4.90: 26301 Nonbonded interactions: 65281 Sorted by model distance: nonbonded pdb=" O LYS B 323 " pdb=" NZ LYS B 385 " model vdw 2.304 3.120 nonbonded pdb=" OH TYR A 457 " pdb=" OD2 ASP A 488 " model vdw 2.361 3.040 nonbonded pdb=" NZ LYS A 104 " pdb=" O LEU A 193 " model vdw 2.364 3.120 nonbonded pdb=" OD1 ASP B 17 " pdb=" N GLY B 18 " model vdw 2.369 3.120 nonbonded pdb=" OE1 GLN A 547 " pdb=" OG1 THR B 286 " model vdw 2.372 3.040 ... (remaining 65276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.960 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 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 : 0.005 0.069 8595 Z= 0.339 Angle : 0.823 14.254 11844 Z= 0.529 Chirality : 0.062 0.371 1304 Planarity : 0.008 0.209 1371 Dihedral : 16.650 88.455 3258 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 1.96 % Allowed : 1.96 % Favored : 96.09 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.28), residues: 921 helix: 0.95 (0.31), residues: 325 sheet: -1.19 (0.39), residues: 171 loop : -0.85 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 284 TYR 0.030 0.002 TYR A 319 PHE 0.007 0.001 PHE A 389 TRP 0.029 0.002 TRP A 402 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.34 ( 8595) covalent geometry : angle 0.82347 / 0.53 (11844) hydrogen bonds : bond 0.13815 / 8.75 ( 322) hydrogen bonds : angle 6.32394 / 4.49 ( 870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.216 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 132 average time/residue: 0.0657 time to fit residues: 12.3820 Evaluate side-chains 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.210877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.166503 restraints weight = 8821.610| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.82 r_work: 0.3691 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8595 Z= 0.173 Angle : 0.627 8.126 11844 Z= 0.339 Chirality : 0.046 0.255 1304 Planarity : 0.005 0.056 1371 Dihedral : 15.300 79.497 1355 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.69 % Favored : 96.09 % Rotamer: Outliers : 0.98 % Allowed : 9.78 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.27), residues: 921 helix: 1.01 (0.30), residues: 327 sheet: -1.11 (0.39), residues: 172 loop : -0.97 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 358 TYR 0.019 0.002 TYR A 339 PHE 0.008 0.001 PHE B 416 TRP 0.024 0.002 TRP A 406 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 8595) covalent geometry : angle 0.62688 / 0.34 (11844) hydrogen bonds : bond 0.04770 / 3.15 ( 322) hydrogen bonds : angle 4.42034 / 3.05 ( 870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 204 GLU cc_start: 0.7157 (mp0) cc_final: 0.6886 (mp0) REVERT: B 212 TRP cc_start: 0.5034 (m-10) cc_final: 0.4791 (t60) REVERT: B 382 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.7887 (mp) outliers start: 8 outliers final: 5 residues processed: 101 average time/residue: 0.0630 time to fit residues: 9.0946 Evaluate side-chains 98 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 43 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 42 optimal weight: 30.0000 chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 1 optimal weight: 30.0000 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 547 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.206382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.162378 restraints weight = 8835.309| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.77 r_work: 0.3641 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8595 Z= 0.214 Angle : 0.639 7.262 11844 Z= 0.344 Chirality : 0.047 0.196 1304 Planarity : 0.005 0.049 1371 Dihedral : 15.504 69.251 1355 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.91 % Favored : 95.98 % Rotamer: Outliers : 2.08 % Allowed : 12.59 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.27), residues: 921 helix: 0.69 (0.29), residues: 330 sheet: -1.20 (0.40), residues: 162 loop : -1.22 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 358 TYR 0.023 0.002 TYR A 339 PHE 0.009 0.002 PHE B 130 TRP 0.017 0.002 TRP A 406 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 ( 8595) covalent geometry : angle 0.63855 / 0.34 (11844) hydrogen bonds : bond 0.04727 / 3.10 ( 322) hydrogen bonds : angle 4.31827 / 2.98 ( 870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8160 (pt0) cc_final: 0.7821 (pt0) REVERT: A 281 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7481 (tttt) REVERT: B 102 LYS cc_start: 0.7412 (mppt) cc_final: 0.6819 (mppt) REVERT: B 382 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.7983 (mp) outliers start: 17 outliers final: 10 residues processed: 107 average time/residue: 0.0829 time to fit residues: 12.5424 Evaluate side-chains 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 73 optimal weight: 30.0000 chunk 81 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.208787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.164415 restraints weight = 8856.497| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.81 r_work: 0.3664 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8595 Z= 0.158 Angle : 0.580 6.812 11844 Z= 0.311 Chirality : 0.044 0.205 1304 Planarity : 0.004 0.045 1371 Dihedral : 15.437 63.199 1355 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.58 % Favored : 96.31 % Rotamer: Outliers : 2.44 % Allowed : 14.43 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.27), residues: 921 helix: 1.01 (0.29), residues: 324 sheet: -1.28 (0.40), residues: 164 loop : -1.10 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.018 0.002 TYR A 339 PHE 0.007 0.001 PHE B 416 TRP 0.026 0.002 TRP B 212 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 8595) covalent geometry : angle 0.57975 / 0.31 (11844) hydrogen bonds : bond 0.04028 / 2.68 ( 322) hydrogen bonds : angle 4.18767 / 2.91 ( 870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8175 (pt0) cc_final: 0.7835 (pt0) REVERT: B 102 LYS cc_start: 0.7292 (mppt) cc_final: 0.6842 (mppt) REVERT: B 203 GLU cc_start: 0.7604 (pp20) cc_final: 0.7383 (pp20) REVERT: B 382 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.7964 (mp) outliers start: 20 outliers final: 12 residues processed: 117 average time/residue: 0.0599 time to fit residues: 10.3080 Evaluate side-chains 103 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 88 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 42 optimal weight: 40.0000 chunk 73 optimal weight: 20.0000 chunk 59 optimal weight: 0.3980 chunk 52 optimal weight: 20.0000 chunk 5 optimal weight: 0.0030 chunk 61 optimal weight: 7.9990 chunk 86 optimal weight: 0.3980 chunk 13 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN A 480 GLN B 363 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.208455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164038 restraints weight = 8821.829| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.82 r_work: 0.3717 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8595 Z= 0.134 Angle : 0.554 6.550 11844 Z= 0.297 Chirality : 0.043 0.206 1304 Planarity : 0.004 0.043 1371 Dihedral : 15.323 59.313 1355 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.26 % Favored : 96.63 % Rotamer: Outliers : 1.96 % Allowed : 16.26 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.27), residues: 921 helix: 1.18 (0.30), residues: 323 sheet: -1.31 (0.39), residues: 174 loop : -0.93 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.022 0.002 TYR A 232 PHE 0.006 0.001 PHE B 416 TRP 0.024 0.001 TRP A 406 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8595) covalent geometry : angle 0.55413 / 0.30 (11844) hydrogen bonds : bond 0.03648 / 2.45 ( 322) hydrogen bonds : angle 4.04460 / 2.81 ( 870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.177 Fit side-chains REVERT: A 182 GLN cc_start: 0.8119 (pt0) cc_final: 0.7751 (pt0) REVERT: B 102 LYS cc_start: 0.7250 (mppt) cc_final: 0.6909 (mppt) REVERT: B 203 GLU cc_start: 0.7596 (pp20) cc_final: 0.7368 (pp20) REVERT: B 382 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.7917 (mp) outliers start: 16 outliers final: 12 residues processed: 118 average time/residue: 0.0739 time to fit residues: 12.3582 Evaluate side-chains 109 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 9.9990 chunk 3 optimal weight: 30.0000 chunk 84 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 5 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 83 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 GLN B 363 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.205005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.161542 restraints weight = 8890.392| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.85 r_work: 0.3650 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8595 Z= 0.219 Angle : 0.639 7.198 11844 Z= 0.340 Chirality : 0.046 0.214 1304 Planarity : 0.005 0.042 1371 Dihedral : 15.538 59.193 1354 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.45 % Favored : 95.44 % Rotamer: Outliers : 2.81 % Allowed : 16.87 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.27), residues: 921 helix: 0.73 (0.29), residues: 324 sheet: -1.49 (0.40), residues: 165 loop : -1.18 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 125 TYR 0.022 0.002 TYR A 339 PHE 0.011 0.002 PHE B 130 TRP 0.019 0.002 TRP A 406 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.22 ( 8595) covalent geometry : angle 0.63937 / 0.34 (11844) hydrogen bonds : bond 0.04502 / 3.00 ( 322) hydrogen bonds : angle 4.23104 / 2.94 ( 870) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.8454 (mmm) cc_final: 0.7781 (tpp) REVERT: A 182 GLN cc_start: 0.8161 (pt0) cc_final: 0.7835 (pt0) REVERT: B 102 LYS cc_start: 0.7293 (mppt) cc_final: 0.6770 (mppt) REVERT: B 203 GLU cc_start: 0.7613 (pp20) cc_final: 0.7382 (pp20) REVERT: B 382 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.7973 (mp) outliers start: 23 outliers final: 19 residues processed: 114 average time/residue: 0.0680 time to fit residues: 11.1640 Evaluate side-chains 113 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 18 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 363 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.210840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.166484 restraints weight = 8800.288| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 1.82 r_work: 0.3701 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8595 Z= 0.126 Angle : 0.550 6.628 11844 Z= 0.294 Chirality : 0.043 0.185 1304 Planarity : 0.004 0.045 1371 Dihedral : 15.271 59.743 1354 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 2.08 % Allowed : 18.22 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.28), residues: 921 helix: 1.12 (0.30), residues: 324 sheet: -1.39 (0.39), residues: 174 loop : -0.99 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.023 0.002 TYR A 232 PHE 0.006 0.001 PHE B 416 TRP 0.022 0.001 TRP A 406 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 8595) covalent geometry : angle 0.55006 / 0.29 (11844) hydrogen bonds : bond 0.03555 / 2.38 ( 322) hydrogen bonds : angle 4.05567 / 2.82 ( 870) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.295 Fit side-chains REVERT: A 182 GLN cc_start: 0.8145 (pt0) cc_final: 0.7820 (pt0) REVERT: B 203 GLU cc_start: 0.7622 (pp20) cc_final: 0.7349 (pp20) REVERT: B 382 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7908 (mp) outliers start: 17 outliers final: 15 residues processed: 114 average time/residue: 0.0807 time to fit residues: 13.1194 Evaluate side-chains 111 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 42 optimal weight: 40.0000 chunk 22 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.207297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.162607 restraints weight = 8784.339| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.81 r_work: 0.3650 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8595 Z= 0.201 Angle : 0.620 7.038 11844 Z= 0.329 Chirality : 0.045 0.186 1304 Planarity : 0.005 0.043 1371 Dihedral : 15.242 58.957 1354 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.22 % Rotamer: Outliers : 2.57 % Allowed : 18.09 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.27), residues: 921 helix: 0.76 (0.29), residues: 328 sheet: -1.46 (0.40), residues: 165 loop : -1.20 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 83 TYR 0.022 0.002 TYR A 339 PHE 0.009 0.002 PHE B 130 TRP 0.022 0.002 TRP A 406 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 ( 8595) covalent geometry : angle 0.62019 / 0.33 (11844) hydrogen bonds : bond 0.04201 / 2.82 ( 322) hydrogen bonds : angle 4.19137 / 2.91 ( 870) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.220 Fit side-chains REVERT: A 182 GLN cc_start: 0.8158 (pt0) cc_final: 0.7852 (pt0) REVERT: B 102 LYS cc_start: 0.7269 (mppt) cc_final: 0.6792 (mppt) REVERT: B 203 GLU cc_start: 0.7622 (pp20) cc_final: 0.7397 (pp20) REVERT: B 382 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.7953 (mp) outliers start: 21 outliers final: 17 residues processed: 115 average time/residue: 0.0725 time to fit residues: 12.0250 Evaluate side-chains 112 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 80 optimal weight: 3.9990 chunk 95 optimal weight: 50.0000 chunk 59 optimal weight: 0.4980 chunk 91 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 21 optimal weight: 0.3980 chunk 64 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.210822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.166131 restraints weight = 8704.309| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 1.83 r_work: 0.3700 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8595 Z= 0.129 Angle : 0.563 7.482 11844 Z= 0.300 Chirality : 0.043 0.172 1304 Planarity : 0.004 0.046 1371 Dihedral : 14.933 59.976 1354 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 2.32 % Allowed : 18.46 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.28), residues: 921 helix: 1.01 (0.29), residues: 328 sheet: -1.35 (0.39), residues: 175 loop : -0.99 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 83 TYR 0.023 0.002 TYR A 232 PHE 0.006 0.001 PHE B 416 TRP 0.025 0.001 TRP A 406 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8595) covalent geometry : angle 0.56316 / 0.30 (11844) hydrogen bonds : bond 0.03525 / 2.35 ( 322) hydrogen bonds : angle 4.15657 / 2.91 ( 870) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.230 Fit side-chains REVERT: A 182 GLN cc_start: 0.8135 (pt0) cc_final: 0.7800 (pt0) REVERT: A 204 GLU cc_start: 0.7712 (mp0) cc_final: 0.7449 (mp0) REVERT: B 40 GLU cc_start: 0.7479 (tt0) cc_final: 0.7246 (tt0) REVERT: B 203 GLU cc_start: 0.7641 (pp20) cc_final: 0.7418 (pp20) REVERT: B 342 TYR cc_start: 0.8046 (p90) cc_final: 0.7497 (p90) REVERT: B 382 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.7944 (mp) outliers start: 19 outliers final: 15 residues processed: 115 average time/residue: 0.0664 time to fit residues: 10.9807 Evaluate side-chains 110 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 78 optimal weight: 0.1980 chunk 4 optimal weight: 0.4980 chunk 86 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN B 363 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.214413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.169891 restraints weight = 8657.166| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.84 r_work: 0.3741 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8595 Z= 0.114 Angle : 0.543 7.641 11844 Z= 0.287 Chirality : 0.042 0.146 1304 Planarity : 0.004 0.046 1371 Dihedral : 14.617 59.762 1353 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 1.59 % Allowed : 18.83 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.28), residues: 921 helix: 1.24 (0.30), residues: 328 sheet: -1.10 (0.40), residues: 175 loop : -0.89 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.020 0.001 TYR A 232 PHE 0.005 0.001 PHE B 416 TRP 0.032 0.001 TRP A 406 HIS 0.002 0.000 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 8595) covalent geometry : angle 0.54300 / 0.29 (11844) hydrogen bonds : bond 0.02987 / 2.03 ( 322) hydrogen bonds : angle 4.01446 / 2.82 ( 870) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.300 Fit side-chains REVERT: A 182 GLN cc_start: 0.8128 (pt0) cc_final: 0.7788 (pt0) REVERT: B 40 GLU cc_start: 0.7409 (tt0) cc_final: 0.7197 (tt0) REVERT: B 203 GLU cc_start: 0.7593 (pp20) cc_final: 0.7392 (pp20) REVERT: B 342 TYR cc_start: 0.7982 (p90) cc_final: 0.7470 (p90) REVERT: B 382 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7865 (mp) outliers start: 13 outliers final: 12 residues processed: 109 average time/residue: 0.0742 time to fit residues: 11.5621 Evaluate side-chains 106 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 21 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 22 optimal weight: 0.0970 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.213437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.169494 restraints weight = 8732.112| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.88 r_work: 0.3728 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8595 Z= 0.119 Angle : 0.546 8.259 11844 Z= 0.289 Chirality : 0.042 0.174 1304 Planarity : 0.004 0.045 1371 Dihedral : 14.617 59.750 1353 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 2.08 % Allowed : 18.95 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.28), residues: 921 helix: 1.24 (0.30), residues: 328 sheet: -1.06 (0.40), residues: 175 loop : -0.89 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 83 TYR 0.020 0.001 TYR A 232 PHE 0.005 0.001 PHE B 416 TRP 0.028 0.001 TRP A 406 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 8595) covalent geometry : angle 0.54609 / 0.29 (11844) hydrogen bonds : bond 0.03116 / 2.12 ( 322) hydrogen bonds : angle 4.04222 / 2.85 ( 870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1783.73 seconds wall clock time: 31 minutes 12.81 seconds (1872.81 seconds total)