Starting phenix.real_space_refine on Fri Sep 11 06:18:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z29_14458/09_2026/7z29_14458.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z29_14458/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7z29_14458/09_2026/7z29_14458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z29_14458/09_2026/7z29_14458.map" model { file = "/net/cci-nas-00/data/ceres_data/7z29_14458/09_2026/7z29_14458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z29_14458/09_2026/7z29_14458.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z29_14458/09_2026/7z29_14458.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z29_14458/09_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-2.2.1-6174/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: 1.67, per 1000 atoms: 0.20 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: 0.79 Conformation dependent library (CDL) restraints added in 246.4 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: 0.83 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: 1.22 Time building geometry restraints manager: 1.03 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=" O3' DC E 3 " pdb=" P OMC E 4 " ideal model delta sigma weight residual 1.607 1.558 0.049 1.20e-02 6.94e+03 1.64e+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 ... (remaining 8590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 11647 2.85 - 5.70: 176 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=" C3' DC E 3 " pdb=" O3' DC E 3 " pdb=" P OMC E 4 " ideal model delta sigma weight residual 119.70 126.58 -6.88 1.20e+00 6.94e-01 3.28e+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 ... (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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.720 Find NCS groups from input model: 0.040 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.420 ------------------------------------------------------------------------------- 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= 0.343 Angle : 0.825 14.254 11844 Z= 0.531 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 0.82491 / 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 : 0.303 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 132 average time/residue: 0.0836 time to fit residues: 15.6019 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 : 0.294 ------------------------------------------------------------------------------- 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** A 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.211542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.167234 restraints weight = 8813.196| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.83 r_work: 0.3689 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8595 Z= 0.173 Angle : 0.629 8.011 11844 Z= 0.339 Chirality : 0.046 0.246 1304 Planarity : 0.005 0.056 1371 Dihedral : 15.298 79.299 1355 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.80 % Favored : 95.98 % 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: -0.49 (0.27), residues: 921 helix: 0.99 (0.30), residues: 327 sheet: -1.12 (0.39), residues: 172 loop : -0.96 (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 0.00383 / 0.17 ( 8595) covalent geometry : angle 0.62864 / 0.34 (11844) hydrogen bonds : bond 0.04823 / 3.19 ( 322) hydrogen bonds : angle 4.40794 / 3.04 ( 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 105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 204 GLU cc_start: 0.7176 (mp0) cc_final: 0.6903 (mp0) REVERT: B 382 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.7887 (mp) outliers start: 8 outliers final: 5 residues processed: 102 average time/residue: 0.0821 time to fit residues: 11.8997 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 : 0.252 ------------------------------------------------------------------------------- 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: 10.0000 chunk 86 optimal weight: 8.9990 chunk 52 optimal weight: 0.0470 chunk 73 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 8 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 1 optimal weight: 0.0870 chunk 14 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 overall best weight: 3.4262 ------------------------------------------------------------------------------- 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 = 0.4350 r_free = 0.4350 target = 0.209649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.165066 restraints weight = 8778.504| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.83 r_work: 0.3684 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8595 Z= 0.158 Angle : 0.581 7.477 11844 Z= 0.313 Chirality : 0.044 0.196 1304 Planarity : 0.004 0.049 1371 Dihedral : 15.303 70.618 1355 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.26 % Favored : 96.63 % Rotamer: Outliers : 1.59 % Allowed : 11.86 % Favored : 86.55 % 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: -0.45 (0.27), residues: 921 helix: 1.06 (0.30), residues: 328 sheet: -0.97 (0.40), residues: 162 loop : -1.06 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 358 TYR 0.018 0.002 TYR A 339 PHE 0.008 0.001 PHE B 416 TRP 0.025 0.002 TRP B 212 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 8595) covalent geometry : angle 0.58088 / 0.31 (11844) hydrogen bonds : bond 0.04127 / 2.72 ( 322) hydrogen bonds : angle 4.19649 / 2.91 ( 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 110 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8072 (pt0) cc_final: 0.7631 (pt0) REVERT: A 281 LYS cc_start: 0.7827 (ttmt) cc_final: 0.7411 (tttt) REVERT: B 102 LYS cc_start: 0.7356 (mppt) cc_final: 0.6800 (mppt) REVERT: B 382 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.7926 (mp) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 0.0817 time to fit residues: 12.4131 Evaluate side-chains 100 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 497 THR Chi-restraints excluded: chain B residue 118 VAL 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 417 VAL 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: 9.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.4351 r_free = 0.4351 target = 0.210118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.165298 restraints weight = 8889.178| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.85 r_work: 0.3714 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8595 Z= 0.129 Angle : 0.544 6.649 11844 Z= 0.293 Chirality : 0.043 0.203 1304 Planarity : 0.004 0.044 1371 Dihedral : 15.245 64.082 1354 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.07 % Rotamer: Outliers : 1.59 % Allowed : 13.33 % Favored : 85.09 % 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: -0.24 (0.27), residues: 921 helix: 1.34 (0.30), residues: 322 sheet: -1.09 (0.39), residues: 174 loop : -0.87 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 125 TYR 0.015 0.001 TYR A 339 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 0.00277 / 0.13 ( 8595) covalent geometry : angle 0.54368 / 0.29 (11844) hydrogen bonds : bond 0.03547 / 2.38 ( 322) hydrogen bonds : angle 4.05012 / 2.83 ( 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 113 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8089 (pt0) cc_final: 0.7674 (pt0) REVERT: B 203 GLU cc_start: 0.7611 (pp20) cc_final: 0.7327 (pp20) REVERT: B 382 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.7893 (mp) outliers start: 13 outliers final: 8 residues processed: 112 average time/residue: 0.0804 time to fit residues: 12.9125 Evaluate side-chains 98 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 417 VAL 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: 6.9990 chunk 78 optimal weight: 20.0000 chunk 42 optimal weight: 40.0000 chunk 73 optimal weight: 0.7980 chunk 59 optimal weight: 0.0000 chunk 52 optimal weight: 8.9990 chunk 5 optimal weight: 0.0970 chunk 61 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.211945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.168215 restraints weight = 8773.063| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.88 r_work: 0.3720 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8595 Z= 0.137 Angle : 0.547 6.566 11844 Z= 0.293 Chirality : 0.043 0.155 1304 Planarity : 0.004 0.042 1371 Dihedral : 15.264 60.031 1353 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 1.47 % Allowed : 14.91 % Favored : 83.62 % 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: -0.24 (0.27), residues: 921 helix: 1.36 (0.30), residues: 323 sheet: -1.14 (0.39), residues: 174 loop : -0.86 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.016 0.002 TYR A 339 PHE 0.007 0.001 PHE B 416 TRP 0.024 0.001 TRP A 406 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 8595) covalent geometry : angle 0.54683 / 0.29 (11844) hydrogen bonds : bond 0.03584 / 2.41 ( 322) hydrogen bonds : angle 3.98308 / 2.78 ( 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 105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.205 Fit side-chains REVERT: A 182 GLN cc_start: 0.8114 (pt0) cc_final: 0.7699 (pt0) REVERT: A 425 LEU cc_start: 0.7916 (mp) cc_final: 0.7580 (mt) REVERT: A 428 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6811 (mm110) REVERT: B 203 GLU cc_start: 0.7601 (pp20) cc_final: 0.7304 (pp20) REVERT: B 382 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.7882 (mp) outliers start: 12 outliers final: 8 residues processed: 101 average time/residue: 0.0808 time to fit residues: 11.5092 Evaluate side-chains 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 428 GLN 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 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 417 VAL 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: 6.9990 chunk 90 optimal weight: 5.9990 chunk 5 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.207664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.163141 restraints weight = 8829.799| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.81 r_work: 0.3677 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1653 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= 0.202 Angle : 0.608 6.952 11844 Z= 0.324 Chirality : 0.045 0.211 1304 Planarity : 0.004 0.042 1371 Dihedral : 15.404 59.600 1353 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.02 % Favored : 95.87 % Rotamer: Outliers : 2.57 % Allowed : 15.77 % Favored : 81.66 % 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: -0.60 (0.27), residues: 921 helix: 1.02 (0.29), residues: 324 sheet: -1.39 (0.38), residues: 175 loop : -1.02 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.028 0.003 TYR A 232 PHE 0.010 0.002 PHE B 130 TRP 0.023 0.002 TRP A 406 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 ( 8595) covalent geometry : angle 0.60839 / 0.32 (11844) hydrogen bonds : bond 0.04170 / 2.79 ( 322) hydrogen bonds : angle 4.10097 / 2.85 ( 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 112 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.340 Fit side-chains REVERT: A 182 GLN cc_start: 0.8156 (pt0) cc_final: 0.7768 (pt0) REVERT: A 204 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7363 (mm-30) REVERT: B 83 ARG cc_start: 0.6948 (mmt180) cc_final: 0.6697 (mmt180) REVERT: B 203 GLU cc_start: 0.7612 (pp20) cc_final: 0.7372 (pp20) REVERT: B 382 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.7945 (mp) outliers start: 21 outliers final: 17 residues processed: 106 average time/residue: 0.0741 time to fit residues: 11.4719 Evaluate side-chains 106 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 409 THR Chi-restraints excluded: chain A residue 497 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 189 VAL Chi-restraints excluded: chain B residue 274 ILE 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 417 VAL 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: 6.9990 chunk 89 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.4313 r_free = 0.4313 target = 0.205931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.163993 restraints weight = 8902.924| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.91 r_work: 0.3641 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8595 Z= 0.213 Angle : 0.626 7.149 11844 Z= 0.333 Chirality : 0.046 0.210 1304 Planarity : 0.005 0.042 1371 Dihedral : 15.450 59.169 1353 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.23 % Favored : 95.66 % Rotamer: Outliers : 2.44 % Allowed : 16.14 % Favored : 81.42 % 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: -0.85 (0.27), residues: 921 helix: 0.80 (0.29), residues: 324 sheet: -1.46 (0.40), residues: 165 loop : -1.20 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 125 TYR 0.024 0.003 TYR A 232 PHE 0.010 0.002 PHE B 130 TRP 0.018 0.002 TRP A 402 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 ( 8595) covalent geometry : angle 0.62587 / 0.33 (11844) hydrogen bonds : bond 0.04404 / 2.94 ( 322) hydrogen bonds : angle 4.19175 / 2.90 ( 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 117 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.303 Fit side-chains REVERT: A 164 MET cc_start: 0.8293 (mmm) cc_final: 0.7597 (tpp) REVERT: A 182 GLN cc_start: 0.8045 (pt0) cc_final: 0.7749 (pt0) REVERT: A 204 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7322 (mm-30) REVERT: B 203 GLU cc_start: 0.7593 (pp20) cc_final: 0.7356 (pp20) REVERT: B 382 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.7927 (mp) outliers start: 20 outliers final: 15 residues processed: 113 average time/residue: 0.0664 time to fit residues: 11.0429 Evaluate side-chains 106 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 409 THR Chi-restraints excluded: chain A residue 497 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 42 optimal weight: 30.0000 chunk 22 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4338 r_free = 0.4338 target = 0.208623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.164092 restraints weight = 8823.074| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.81 r_work: 0.3693 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8595 Z= 0.147 Angle : 0.563 6.759 11844 Z= 0.299 Chirality : 0.043 0.198 1304 Planarity : 0.004 0.046 1371 Dihedral : 15.123 59.937 1353 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 2.08 % Allowed : 17.11 % Favored : 80.81 % 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: -0.63 (0.27), residues: 921 helix: 1.06 (0.29), residues: 324 sheet: -1.46 (0.38), residues: 175 loop : -1.06 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 356 TYR 0.023 0.002 TYR A 232 PHE 0.006 0.001 PHE B 416 TRP 0.020 0.001 TRP A 406 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 8595) covalent geometry : angle 0.56275 / 0.30 (11844) hydrogen bonds : bond 0.03718 / 2.49 ( 322) hydrogen bonds : angle 4.05946 / 2.82 ( 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 116 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.225 Fit side-chains REVERT: A 164 MET cc_start: 0.8313 (mmm) cc_final: 0.8065 (tpp) REVERT: A 182 GLN cc_start: 0.8120 (pt0) cc_final: 0.7788 (pt0) REVERT: A 204 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7441 (mm-30) REVERT: B 83 ARG cc_start: 0.6913 (mmt180) cc_final: 0.6708 (mmt180) REVERT: B 203 GLU cc_start: 0.7641 (pp20) cc_final: 0.7405 (pp20) REVERT: B 342 TYR cc_start: 0.8048 (p90) cc_final: 0.7557 (p90) REVERT: B 382 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.7960 (mp) outliers start: 17 outliers final: 13 residues processed: 112 average time/residue: 0.0804 time to fit residues: 12.7767 Evaluate side-chains 109 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL 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 409 THR 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 189 VAL 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: 10.0000 chunk 29 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 80 optimal weight: 0.8980 chunk 95 optimal weight: 50.0000 chunk 59 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 1 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.206862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.163607 restraints weight = 8833.429| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.86 r_work: 0.3672 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8595 Z= 0.160 Angle : 0.584 7.349 11844 Z= 0.307 Chirality : 0.044 0.183 1304 Planarity : 0.004 0.045 1371 Dihedral : 14.917 59.425 1353 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.80 % Favored : 96.09 % Rotamer: Outliers : 2.08 % Allowed : 17.48 % Favored : 80.44 % 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: -0.66 (0.27), residues: 921 helix: 0.99 (0.29), residues: 323 sheet: -1.43 (0.38), residues: 175 loop : -1.07 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 356 TYR 0.021 0.002 TYR A 232 PHE 0.007 0.001 PHE B 130 TRP 0.022 0.002 TRP A 406 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 8595) covalent geometry : angle 0.58425 / 0.31 (11844) hydrogen bonds : bond 0.03794 / 2.56 ( 322) hydrogen bonds : angle 4.06228 / 2.83 ( 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 113 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.208 Fit side-chains REVERT: A 164 MET cc_start: 0.8114 (mmm) cc_final: 0.7682 (tpp) REVERT: A 182 GLN cc_start: 0.8131 (pt0) cc_final: 0.7734 (pt0) REVERT: A 204 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7446 (mm-30) REVERT: B 83 ARG cc_start: 0.6966 (mmt180) cc_final: 0.6766 (mmt180) REVERT: B 203 GLU cc_start: 0.7634 (pp20) cc_final: 0.7399 (pp20) REVERT: B 342 TYR cc_start: 0.8142 (p90) cc_final: 0.7677 (p90) REVERT: B 382 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.7965 (mp) outliers start: 17 outliers final: 15 residues processed: 109 average time/residue: 0.0758 time to fit residues: 11.8753 Evaluate side-chains 109 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL 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 409 THR 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 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: 1.9990 chunk 4 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 19 optimal weight: 0.0670 chunk 31 optimal weight: 1.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.209950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.165285 restraints weight = 8746.319| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.82 r_work: 0.3737 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1889 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= 0.113 Angle : 0.535 6.987 11844 Z= 0.281 Chirality : 0.042 0.162 1304 Planarity : 0.004 0.046 1371 Dihedral : 14.647 59.589 1353 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.71 % Favored : 97.18 % Rotamer: Outliers : 1.47 % Allowed : 18.46 % Favored : 80.07 % 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: -0.27 (0.28), residues: 921 helix: 1.33 (0.30), residues: 326 sheet: -1.18 (0.39), residues: 174 loop : -0.88 (0.29), residues: 421 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 0.031 0.001 TRP A 406 HIS 0.002 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 8595) covalent geometry : angle 0.53513 / 0.28 (11844) hydrogen bonds : bond 0.03066 / 2.09 ( 322) hydrogen bonds : angle 3.93558 / 2.75 ( 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 109 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.266 Fit side-chains REVERT: A 164 MET cc_start: 0.8029 (mmm) cc_final: 0.7656 (tpp) REVERT: A 182 GLN cc_start: 0.8107 (pt0) cc_final: 0.7717 (pt0) REVERT: A 204 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7389 (mm-30) REVERT: B 203 GLU cc_start: 0.7591 (pp20) cc_final: 0.7376 (pp20) REVERT: B 342 TYR cc_start: 0.8026 (p90) cc_final: 0.7588 (p90) REVERT: B 382 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7909 (mp) outliers start: 12 outliers final: 10 residues processed: 107 average time/residue: 0.0775 time to fit residues: 11.8017 Evaluate side-chains 104 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL 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 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 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 21 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4362 r_free = 0.4362 target = 0.211135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.166555 restraints weight = 8753.098| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.82 r_work: 0.3705 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1908 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= 0.136 Angle : 0.554 6.734 11844 Z= 0.291 Chirality : 0.042 0.159 1304 Planarity : 0.004 0.045 1371 Dihedral : 14.681 59.787 1353 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer: Outliers : 1.47 % Allowed : 19.07 % Favored : 79.46 % 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: -0.35 (0.28), residues: 921 helix: 1.29 (0.30), residues: 326 sheet: -1.25 (0.39), residues: 175 loop : -0.94 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 83 TYR 0.021 0.002 TYR A 232 PHE 0.006 0.001 PHE B 130 TRP 0.024 0.001 TRP A 406 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 8595) covalent geometry : angle 0.55375 / 0.29 (11844) hydrogen bonds : bond 0.03375 / 2.30 ( 322) hydrogen bonds : angle 3.94611 / 2.76 ( 870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1949.69 seconds wall clock time: 34 minutes 1.95 seconds (2041.95 seconds total)