Starting phenix.real_space_refine on Sun Apr 5 17:21:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ux8_64576/04_2026/9ux8_64576.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ux8_64576/04_2026/9ux8_64576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ux8_64576/04_2026/9ux8_64576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ux8_64576/04_2026/9ux8_64576.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ux8_64576/04_2026/9ux8_64576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ux8_64576/04_2026/9ux8_64576.map" } resolution = 3.71 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 7573 2.51 5 N 1936 2.21 5 O 2273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11820 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4682 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 555} Chain: "B" Number of atoms: 4682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4682 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 555} Chain: "C" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2456 Classifications: {'peptide': 304} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 294} Time building chain proxies: 2.67, per 1000 atoms: 0.23 Number of scatterers: 11820 At special positions: 0 Unit cell: (103.32, 124.64, 146.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 2273 8.00 N 1936 7.00 C 7573 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: 0.95 Conformation dependent library (CDL) restraints added in 561.7 milliseconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2790 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 8 sheets defined 60.4% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 36 through 48 removed outlier: 3.516A pdb=" N LEU A 48 " --> pdb=" O MET A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 108 Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 173 through 211 Processing helix chain 'A' and resid 223 through 276 Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.972A pdb=" N LEU A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 351 Processing helix chain 'A' and resid 357 through 429 removed outlier: 3.691A pdb=" N TYR A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 480 removed outlier: 3.747A pdb=" N LYS A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 512 removed outlier: 3.574A pdb=" N LYS A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 removed outlier: 4.219A pdb=" N LYS A 528 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 556 removed outlier: 4.085A pdb=" N LEU A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 47 Processing helix chain 'B' and resid 96 through 108 Processing helix chain 'B' and resid 126 through 132 removed outlier: 3.629A pdb=" N VAL B 130 " --> pdb=" O TYR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 176 through 211 Processing helix chain 'B' and resid 225 through 281 Processing helix chain 'B' and resid 294 through 299 Processing helix chain 'B' and resid 299 through 351 removed outlier: 3.503A pdb=" N ASN B 351 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 428 removed outlier: 4.011A pdb=" N ASP B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 Processing helix chain 'B' and resid 442 through 446 removed outlier: 3.629A pdb=" N LEU B 446 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 480 Processing helix chain 'B' and resid 498 through 512 Processing helix chain 'B' and resid 525 through 530 removed outlier: 4.064A pdb=" N LYS B 528 " --> pdb=" O GLU B 525 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 530 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 550 through 558 removed outlier: 3.704A pdb=" N LYS B 557 " --> pdb=" O GLU B 553 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 29 removed outlier: 3.942A pdb=" N ILE C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 70 Processing helix chain 'C' and resid 71 through 76 removed outlier: 7.632A pdb=" N SER C 74 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 85 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 157 through 172 Processing helix chain 'C' and resid 177 through 198 removed outlier: 3.576A pdb=" N ALA C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 210 removed outlier: 3.770A pdb=" N LYS C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 236 removed outlier: 5.210A pdb=" N ASP C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 251 removed outlier: 3.686A pdb=" N LYS C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 268 Processing helix chain 'C' and resid 269 through 276 removed outlier: 3.703A pdb=" N LEU C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 293 Processing helix chain 'C' and resid 300 through 315 removed outlier: 4.047A pdb=" N GLU C 315 " --> pdb=" O CYS C 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.963A pdb=" N GLU A 69 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHE A 6 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLN A 67 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE A 8 " --> pdb=" O TYR A 65 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N TYR A 65 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL A 88 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL A 93 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 486 through 488 removed outlier: 3.867A pdb=" N SER A 521 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLY A 24 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE A 520 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASN A 26 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE A 522 " --> pdb=" O ASN A 26 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE A 28 " --> pdb=" O ILE A 522 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 20 removed outlier: 5.973A pdb=" N ILE B 3 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU B 71 " --> pdb=" O ILE B 3 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 135 through 136 removed outlier: 6.214A pdb=" N PHE B 486 " --> pdb=" O PHE B 519 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N SER B 521 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N MET B 488 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N VAL B 523 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 30 " --> pdb=" O ILE B 522 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR B 25 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE B 539 " --> pdb=" O THR B 25 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B 27 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 124 removed outlier: 4.579A pdb=" N ALA B 115 " --> pdb=" O THR B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 147 through 151 removed outlier: 6.668A pdb=" N ARG C 93 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N TYR C 150 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE C 95 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N THR C 53 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LYS C 94 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE C 55 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE C 96 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN C 57 " --> pdb=" O PHE C 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 109 through 112 728 hydrogen bonds defined for protein. 2118 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3799 1.34 - 1.46: 2305 1.46 - 1.58: 5833 1.58 - 1.70: 0 1.70 - 1.81: 68 Bond restraints: 12005 Sorted by residual: bond pdb=" CB ARG C 194 " pdb=" CG ARG C 194 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.31e+00 bond pdb=" C SER C 85 " pdb=" N PRO C 86 " ideal model delta sigma weight residual 1.328 1.348 -0.020 1.26e-02 6.30e+03 2.52e+00 bond pdb=" CB MET B 273 " pdb=" CG MET B 273 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" CG1 ILE B 471 " pdb=" CD1 ILE B 471 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.11e+00 bond pdb=" CG ARG C 208 " pdb=" CD ARG C 208 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.08e+00 ... (remaining 12000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 15921 2.41 - 4.81: 188 4.81 - 7.22: 25 7.22 - 9.63: 2 9.63 - 12.03: 1 Bond angle restraints: 16137 Sorted by residual: angle pdb=" C SER A 304 " pdb=" CA SER A 304 " pdb=" CB SER A 304 " ideal model delta sigma weight residual 116.54 110.13 6.41 1.15e+00 7.56e-01 3.10e+01 angle pdb=" N LYS B 493 " pdb=" CA LYS B 493 " pdb=" C LYS B 493 " ideal model delta sigma weight residual 114.04 107.56 6.48 1.24e+00 6.50e-01 2.73e+01 angle pdb=" N VAL C 176 " pdb=" CA VAL C 176 " pdb=" C VAL C 176 " ideal model delta sigma weight residual 113.47 108.84 4.63 1.01e+00 9.80e-01 2.10e+01 angle pdb=" N LEU C 115 " pdb=" CA LEU C 115 " pdb=" C LEU C 115 " ideal model delta sigma weight residual 113.89 107.24 6.65 1.58e+00 4.01e-01 1.77e+01 angle pdb=" CB MET B 273 " pdb=" CG MET B 273 " pdb=" SD MET B 273 " ideal model delta sigma weight residual 112.70 100.67 12.03 3.00e+00 1.11e-01 1.61e+01 ... (remaining 16132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 6650 17.71 - 35.43: 632 35.43 - 53.14: 97 53.14 - 70.85: 35 70.85 - 88.57: 29 Dihedral angle restraints: 7443 sinusoidal: 3163 harmonic: 4280 Sorted by residual: dihedral pdb=" CA SER A 218 " pdb=" C SER A 218 " pdb=" N LYS A 219 " pdb=" CA LYS A 219 " ideal model delta harmonic sigma weight residual 180.00 155.37 24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA THR B 283 " pdb=" C THR B 283 " pdb=" N GLU B 284 " pdb=" CA GLU B 284 " ideal model delta harmonic sigma weight residual 180.00 155.72 24.28 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ARG B 548 " pdb=" C ARG B 548 " pdb=" N ASP B 549 " pdb=" CA ASP B 549 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 7440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1337 0.043 - 0.087: 376 0.087 - 0.130: 102 0.130 - 0.173: 8 0.173 - 0.217: 2 Chirality restraints: 1825 Sorted by residual: chirality pdb=" CG LEU C 183 " pdb=" CB LEU C 183 " pdb=" CD1 LEU C 183 " pdb=" CD2 LEU C 183 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ASP A 221 " pdb=" N ASP A 221 " pdb=" C ASP A 221 " pdb=" CB ASP A 221 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA ILE B 484 " pdb=" N ILE B 484 " pdb=" C ILE B 484 " pdb=" CB ILE B 484 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.39e-01 ... (remaining 1822 not shown) Planarity restraints: 2043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 484 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO B 485 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 369 " 0.011 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" CD GLU A 369 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLU A 369 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU A 369 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 194 " -0.169 9.50e-02 1.11e+02 7.59e-02 3.56e+00 pdb=" NE ARG C 194 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG C 194 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 194 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 194 " -0.007 2.00e-02 2.50e+03 ... (remaining 2040 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 135 2.64 - 3.21: 11457 3.21 - 3.77: 18707 3.77 - 4.34: 25235 4.34 - 4.90: 41574 Nonbonded interactions: 97108 Sorted by model distance: nonbonded pdb=" O THR B 283 " pdb=" NH2 ARG C 194 " model vdw 2.081 3.120 nonbonded pdb=" OH TYR B 45 " pdb=" O PRO B 485 " model vdw 2.087 3.040 nonbonded pdb=" OH TYR A 361 " pdb=" OE1 GLN B 236 " model vdw 2.165 3.040 nonbonded pdb=" O ILE A 164 " pdb=" OG SER A 167 " model vdw 2.183 3.040 nonbonded pdb=" OE2 GLU C 107 " pdb=" NE2 GLN C 126 " model vdw 2.193 3.120 ... (remaining 97103 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.600 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 : 0.004 0.075 12005 Z= 0.163 Angle : 0.677 12.032 16137 Z= 0.385 Chirality : 0.043 0.217 1825 Planarity : 0.004 0.101 2043 Dihedral : 15.303 88.566 4653 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.59 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.29 (0.23), residues: 1422 helix: 1.93 (0.18), residues: 800 sheet: 0.66 (0.44), residues: 148 loop : -0.96 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 208 TYR 0.025 0.002 TYR B 287 PHE 0.031 0.002 PHE B 448 TRP 0.010 0.001 TRP B 59 HIS 0.008 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00355 (12005) covalent geometry : angle 0.67731 (16137) hydrogen bonds : bond 0.10548 ( 728) hydrogen bonds : angle 5.37447 ( 2118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ILE cc_start: 0.8740 (pt) cc_final: 0.8367 (pt) REVERT: B 64 MET cc_start: 0.6440 (mmm) cc_final: 0.5724 (mmm) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1063 time to fit residues: 32.0916 Evaluate side-chains 145 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.0270 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 50.0000 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 274 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.179377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.132414 restraints weight = 22494.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.128318 restraints weight = 20043.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.128319 restraints weight = 16207.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.129191 restraints weight = 14437.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.129905 restraints weight = 12741.041| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12005 Z= 0.141 Angle : 0.579 12.171 16137 Z= 0.309 Chirality : 0.042 0.180 1825 Planarity : 0.004 0.062 2043 Dihedral : 4.607 22.332 1534 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.73 % Favored : 96.06 % Rotamer: Outliers : 0.59 % Allowed : 9.45 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.38 (0.22), residues: 1422 helix: 2.06 (0.18), residues: 808 sheet: 0.59 (0.44), residues: 141 loop : -1.04 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 87 TYR 0.026 0.002 TYR B 45 PHE 0.024 0.002 PHE B 560 TRP 0.008 0.001 TRP B 59 HIS 0.009 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00315 (12005) covalent geometry : angle 0.57899 (16137) hydrogen bonds : bond 0.04257 ( 728) hydrogen bonds : angle 4.54047 ( 2118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 171 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 VAL cc_start: 0.9094 (t) cc_final: 0.8887 (p) REVERT: B 106 HIS cc_start: 0.7523 (t-90) cc_final: 0.7138 (t-170) REVERT: B 344 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7673 (pp20) REVERT: C 182 LYS cc_start: 0.8251 (tppt) cc_final: 0.8003 (tptt) outliers start: 8 outliers final: 2 residues processed: 176 average time/residue: 0.1132 time to fit residues: 28.9962 Evaluate side-chains 146 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain B residue 69 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN B 33 ASN ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.177873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.117683 restraints weight = 22444.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.120445 restraints weight = 13901.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.122738 restraints weight = 10375.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.123818 restraints weight = 8530.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124751 restraints weight = 7658.851| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12005 Z= 0.181 Angle : 0.585 10.892 16137 Z= 0.310 Chirality : 0.042 0.180 1825 Planarity : 0.004 0.058 2043 Dihedral : 4.601 23.434 1534 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.94 % Favored : 95.85 % Rotamer: Outliers : 1.40 % Allowed : 10.71 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.29 (0.22), residues: 1422 helix: 2.07 (0.18), residues: 797 sheet: 0.26 (0.43), residues: 145 loop : -1.07 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 72 TYR 0.025 0.002 TYR B 45 PHE 0.024 0.002 PHE B 448 TRP 0.010 0.001 TRP B 59 HIS 0.009 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00420 (12005) covalent geometry : angle 0.58550 (16137) hydrogen bonds : bond 0.04203 ( 728) hydrogen bonds : angle 4.44028 ( 2118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.6426 (m-80) cc_final: 0.6129 (m-80) REVERT: A 177 LEU cc_start: 0.8892 (pp) cc_final: 0.8673 (pp) REVERT: A 193 VAL cc_start: 0.9268 (t) cc_final: 0.9013 (p) REVERT: B 344 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7476 (pp20) REVERT: C 144 MET cc_start: 0.9108 (mmm) cc_final: 0.8895 (mmm) REVERT: C 182 LYS cc_start: 0.8343 (tppt) cc_final: 0.8132 (tptt) outliers start: 19 outliers final: 9 residues processed: 174 average time/residue: 0.1143 time to fit residues: 28.9566 Evaluate side-chains 151 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 290 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 19 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 46 optimal weight: 30.0000 chunk 3 optimal weight: 30.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 387 ASN ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.177770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.131339 restraints weight = 22066.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.127399 restraints weight = 15869.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.127751 restraints weight = 13321.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.128782 restraints weight = 11785.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.129108 restraints weight = 10516.602| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12005 Z= 0.175 Angle : 0.588 10.224 16137 Z= 0.312 Chirality : 0.042 0.147 1825 Planarity : 0.004 0.055 2043 Dihedral : 4.535 22.544 1534 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.36 % Favored : 95.43 % Rotamer: Outliers : 1.99 % Allowed : 12.56 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.29 (0.23), residues: 1422 helix: 2.10 (0.18), residues: 799 sheet: 0.16 (0.43), residues: 145 loop : -1.10 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 208 TYR 0.023 0.001 TYR B 45 PHE 0.017 0.002 PHE B 448 TRP 0.010 0.001 TRP B 59 HIS 0.008 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00405 (12005) covalent geometry : angle 0.58759 (16137) hydrogen bonds : bond 0.04117 ( 728) hydrogen bonds : angle 4.34675 ( 2118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.2460 (OUTLIER) cc_final: 0.2011 (p) REVERT: A 193 VAL cc_start: 0.9084 (t) cc_final: 0.8883 (p) REVERT: B 344 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7593 (pp20) REVERT: B 463 LYS cc_start: 0.7612 (ttpt) cc_final: 0.7366 (ttpt) REVERT: C 148 TYR cc_start: 0.8082 (m-10) cc_final: 0.7816 (m-10) REVERT: C 182 LYS cc_start: 0.8360 (tppt) cc_final: 0.8103 (tptt) REVERT: C 228 MET cc_start: 0.8479 (ppp) cc_final: 0.8049 (ppp) REVERT: C 279 GLU cc_start: 0.8067 (tp30) cc_final: 0.7844 (tp30) outliers start: 27 outliers final: 15 residues processed: 178 average time/residue: 0.1102 time to fit residues: 28.7632 Evaluate side-chains 173 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 290 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 97 optimal weight: 0.8980 chunk 57 optimal weight: 0.0670 chunk 24 optimal weight: 0.5980 chunk 54 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 70 optimal weight: 0.0670 chunk 124 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 HIS B 350 GLN ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.179823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.140463 restraints weight = 22526.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.141432 restraints weight = 23883.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.142203 restraints weight = 20820.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.143185 restraints weight = 12883.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.144173 restraints weight = 10925.592| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12005 Z= 0.120 Angle : 0.582 14.644 16137 Z= 0.302 Chirality : 0.041 0.159 1825 Planarity : 0.003 0.043 2043 Dihedral : 4.385 22.246 1534 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.94 % Favored : 95.85 % Rotamer: Outliers : 1.62 % Allowed : 13.81 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.47 (0.23), residues: 1422 helix: 2.26 (0.18), residues: 798 sheet: 0.07 (0.41), residues: 155 loop : -1.01 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 208 TYR 0.024 0.001 TYR C 150 PHE 0.015 0.001 PHE A 451 TRP 0.006 0.001 TRP B 142 HIS 0.008 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00261 (12005) covalent geometry : angle 0.58194 (16137) hydrogen bonds : bond 0.03887 ( 728) hydrogen bonds : angle 4.23549 ( 2118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.3082 (OUTLIER) cc_final: 0.1903 (p) REVERT: A 165 PHE cc_start: 0.7936 (m-10) cc_final: 0.7595 (m-10) REVERT: B 106 HIS cc_start: 0.7666 (t-90) cc_final: 0.7254 (t-170) REVERT: B 344 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7438 (pp20) REVERT: B 504 MET cc_start: 0.7484 (mmm) cc_final: 0.7277 (mmt) REVERT: B 556 LEU cc_start: 0.8559 (mt) cc_final: 0.8323 (tp) REVERT: C 228 MET cc_start: 0.8516 (ppp) cc_final: 0.8069 (ppp) REVERT: C 259 ASN cc_start: 0.8899 (t0) cc_final: 0.8616 (t0) outliers start: 22 outliers final: 11 residues processed: 191 average time/residue: 0.1040 time to fit residues: 29.6026 Evaluate side-chains 167 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 276 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 132 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 54 optimal weight: 40.0000 chunk 138 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 113 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 30.0000 chunk 74 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 350 GLN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 HIS C 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.174830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.116452 restraints weight = 22212.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115575 restraints weight = 17322.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.117111 restraints weight = 14304.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.117795 restraints weight = 11309.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118116 restraints weight = 10379.412| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12005 Z= 0.244 Angle : 0.683 13.987 16137 Z= 0.352 Chirality : 0.044 0.144 1825 Planarity : 0.004 0.076 2043 Dihedral : 4.544 22.998 1534 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.43 % Favored : 95.36 % Rotamer: Outliers : 2.14 % Allowed : 14.48 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.24 (0.23), residues: 1422 helix: 2.02 (0.18), residues: 802 sheet: 0.11 (0.43), residues: 143 loop : -1.06 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 194 TYR 0.021 0.002 TYR B 45 PHE 0.039 0.002 PHE C 30 TRP 0.018 0.002 TRP A 103 HIS 0.006 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00570 (12005) covalent geometry : angle 0.68271 (16137) hydrogen bonds : bond 0.04366 ( 728) hydrogen bonds : angle 4.45320 ( 2118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8430 (t0) REVERT: B 14 LYS cc_start: 0.7404 (tmtt) cc_final: 0.7108 (tttp) REVERT: B 177 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7604 (mm) REVERT: B 182 SER cc_start: 0.8735 (m) cc_final: 0.8443 (t) REVERT: B 344 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7754 (pp20) REVERT: B 345 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.7912 (tt) REVERT: B 348 ARG cc_start: 0.8419 (tmm-80) cc_final: 0.8197 (ttp80) REVERT: B 556 LEU cc_start: 0.8645 (mt) cc_final: 0.8397 (tp) REVERT: C 259 ASN cc_start: 0.8895 (t0) cc_final: 0.8600 (t0) outliers start: 29 outliers final: 17 residues processed: 180 average time/residue: 0.1007 time to fit residues: 27.2507 Evaluate side-chains 163 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 190 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 6 optimal weight: 40.0000 chunk 121 optimal weight: 40.0000 chunk 133 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 180 GLN A 350 GLN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN B 346 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.176851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.126158 restraints weight = 21831.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.123107 restraints weight = 19708.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123798 restraints weight = 13541.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.124614 restraints weight = 11831.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.124885 restraints weight = 11259.268| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12005 Z= 0.169 Angle : 0.637 14.006 16137 Z= 0.330 Chirality : 0.043 0.196 1825 Planarity : 0.003 0.059 2043 Dihedral : 4.462 22.270 1534 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.29 % Favored : 95.50 % Rotamer: Outliers : 1.99 % Allowed : 15.51 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.27 (0.23), residues: 1422 helix: 2.08 (0.18), residues: 799 sheet: -0.09 (0.43), residues: 145 loop : -1.00 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 194 TYR 0.026 0.001 TYR C 150 PHE 0.033 0.002 PHE C 30 TRP 0.009 0.001 TRP A 103 HIS 0.009 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00391 (12005) covalent geometry : angle 0.63692 (16137) hydrogen bonds : bond 0.04118 ( 728) hydrogen bonds : angle 4.34766 ( 2118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8278 (t0) REVERT: B 14 LYS cc_start: 0.7371 (tmtt) cc_final: 0.7126 (tttp) REVERT: B 64 MET cc_start: 0.7025 (mmm) cc_final: 0.6787 (mmm) REVERT: B 177 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7550 (mm) REVERT: B 178 GLU cc_start: 0.7958 (pt0) cc_final: 0.7716 (pt0) REVERT: B 181 ASN cc_start: 0.7755 (m-40) cc_final: 0.7512 (m-40) REVERT: B 182 SER cc_start: 0.8486 (m) cc_final: 0.8268 (t) REVERT: B 344 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7738 (pp20) REVERT: B 556 LEU cc_start: 0.8612 (mt) cc_final: 0.8397 (tp) REVERT: C 141 LYS cc_start: 0.9334 (pttt) cc_final: 0.9079 (ptpt) REVERT: C 228 MET cc_start: 0.8478 (ppp) cc_final: 0.8102 (ppp) REVERT: C 259 ASN cc_start: 0.8857 (t0) cc_final: 0.8359 (t0) REVERT: C 263 GLN cc_start: 0.8162 (mt0) cc_final: 0.7848 (mt0) REVERT: C 279 GLU cc_start: 0.8164 (tp30) cc_final: 0.7818 (tp30) outliers start: 27 outliers final: 13 residues processed: 174 average time/residue: 0.1050 time to fit residues: 27.2512 Evaluate side-chains 155 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 290 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 43 optimal weight: 20.0000 chunk 1 optimal weight: 50.0000 chunk 109 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 HIS C 18 GLN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.173268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116842 restraints weight = 22721.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.117039 restraints weight = 16884.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.116482 restraints weight = 12384.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.116909 restraints weight = 11731.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.117161 restraints weight = 10730.254| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 12005 Z= 0.278 Angle : 0.731 15.006 16137 Z= 0.377 Chirality : 0.046 0.199 1825 Planarity : 0.004 0.080 2043 Dihedral : 4.647 22.549 1534 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.43 % Favored : 95.36 % Rotamer: Outliers : 2.14 % Allowed : 15.66 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.91 (0.22), residues: 1422 helix: 1.72 (0.18), residues: 806 sheet: -0.05 (0.43), residues: 143 loop : -1.15 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 208 TYR 0.023 0.002 TYR C 17 PHE 0.030 0.002 PHE C 30 TRP 0.010 0.001 TRP B 59 HIS 0.006 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00651 (12005) covalent geometry : angle 0.73138 (16137) hydrogen bonds : bond 0.04539 ( 728) hydrogen bonds : angle 4.57227 ( 2118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8503 (t0) REVERT: A 369 GLU cc_start: 0.8090 (pp20) cc_final: 0.7749 (pp20) REVERT: A 375 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7357 (tp30) REVERT: B 18 ASN cc_start: 0.8104 (t0) cc_final: 0.7453 (p0) REVERT: B 177 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7477 (mm) REVERT: B 178 GLU cc_start: 0.8249 (pt0) cc_final: 0.8027 (pt0) REVERT: B 181 ASN cc_start: 0.7954 (m-40) cc_final: 0.7637 (m-40) REVERT: B 182 SER cc_start: 0.8758 (m) cc_final: 0.8497 (t) REVERT: B 344 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7821 (pp20) REVERT: B 345 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.7829 (tt) REVERT: B 400 ASN cc_start: 0.8726 (m110) cc_final: 0.8482 (m110) REVERT: B 556 LEU cc_start: 0.8665 (mt) cc_final: 0.8399 (tp) REVERT: C 12 LEU cc_start: 0.8050 (tp) cc_final: 0.7782 (tp) REVERT: C 225 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8121 (mm-40) REVERT: C 228 MET cc_start: 0.8546 (ppp) cc_final: 0.8037 (tmm) outliers start: 29 outliers final: 20 residues processed: 168 average time/residue: 0.0931 time to fit residues: 23.8472 Evaluate side-chains 165 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 290 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 55 optimal weight: 40.0000 chunk 117 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 0.0870 chunk 90 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 HIS ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.177292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.125881 restraints weight = 22119.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.123741 restraints weight = 19042.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.123483 restraints weight = 15833.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.124561 restraints weight = 13352.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124948 restraints weight = 11648.697| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12005 Z= 0.159 Angle : 0.667 16.916 16137 Z= 0.340 Chirality : 0.043 0.173 1825 Planarity : 0.003 0.045 2043 Dihedral : 4.520 22.835 1534 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.22 % Favored : 95.57 % Rotamer: Outliers : 1.92 % Allowed : 16.69 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.13 (0.23), residues: 1422 helix: 1.95 (0.18), residues: 806 sheet: -0.21 (0.43), residues: 145 loop : -1.06 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 194 TYR 0.029 0.001 TYR C 150 PHE 0.030 0.002 PHE C 30 TRP 0.009 0.001 TRP B 142 HIS 0.007 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00367 (12005) covalent geometry : angle 0.66735 (16137) hydrogen bonds : bond 0.04127 ( 728) hydrogen bonds : angle 4.38696 ( 2118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.2192 (mmm) cc_final: 0.0959 (mtt) REVERT: A 165 PHE cc_start: 0.8726 (m-10) cc_final: 0.8273 (m-10) REVERT: A 193 VAL cc_start: 0.9112 (t) cc_final: 0.8909 (p) REVERT: A 202 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8339 (t0) REVERT: A 375 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7179 (tp30) REVERT: B 18 ASN cc_start: 0.8033 (t0) cc_final: 0.7455 (p0) REVERT: B 64 MET cc_start: 0.6881 (mmm) cc_final: 0.6619 (mmm) REVERT: B 177 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7485 (mm) REVERT: B 178 GLU cc_start: 0.7992 (pt0) cc_final: 0.7752 (pt0) REVERT: B 181 ASN cc_start: 0.7837 (m-40) cc_final: 0.7599 (m-40) REVERT: B 182 SER cc_start: 0.8545 (m) cc_final: 0.8318 (t) REVERT: B 344 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8028 (tm-30) REVERT: B 345 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8317 (tp) REVERT: B 556 LEU cc_start: 0.8608 (mt) cc_final: 0.8405 (tp) REVERT: C 12 LEU cc_start: 0.7923 (tp) cc_final: 0.7649 (tp) REVERT: C 194 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.7186 (mtt180) REVERT: C 228 MET cc_start: 0.8523 (ppp) cc_final: 0.8013 (tmm) outliers start: 26 outliers final: 16 residues processed: 168 average time/residue: 0.0973 time to fit residues: 24.6044 Evaluate side-chains 167 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 138 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 77 optimal weight: 0.0770 chunk 95 optimal weight: 7.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 HIS ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.176698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.125909 restraints weight = 22908.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.119700 restraints weight = 15468.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.121463 restraints weight = 15394.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.122018 restraints weight = 12004.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.122312 restraints weight = 11555.121| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12005 Z= 0.157 Angle : 0.673 16.922 16137 Z= 0.341 Chirality : 0.043 0.178 1825 Planarity : 0.003 0.049 2043 Dihedral : 4.460 23.085 1534 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.08 % Favored : 95.71 % Rotamer: Outliers : 1.70 % Allowed : 16.99 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.15 (0.23), residues: 1422 helix: 1.98 (0.18), residues: 806 sheet: -0.25 (0.42), residues: 145 loop : -1.06 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 194 TYR 0.023 0.001 TYR B 45 PHE 0.030 0.002 PHE C 30 TRP 0.011 0.001 TRP C 98 HIS 0.008 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00363 (12005) covalent geometry : angle 0.67321 (16137) hydrogen bonds : bond 0.04055 ( 728) hydrogen bonds : angle 4.35543 ( 2118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8851 (m-10) cc_final: 0.8349 (m-10) REVERT: A 193 VAL cc_start: 0.9178 (t) cc_final: 0.8962 (p) REVERT: A 202 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8365 (t0) REVERT: A 375 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7247 (tp30) REVERT: B 64 MET cc_start: 0.7100 (mmm) cc_final: 0.6834 (mmm) REVERT: B 106 HIS cc_start: 0.7534 (t-90) cc_final: 0.7222 (t-170) REVERT: B 177 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7461 (mm) REVERT: B 178 GLU cc_start: 0.8087 (pt0) cc_final: 0.7839 (pt0) REVERT: B 181 ASN cc_start: 0.7933 (m-40) cc_final: 0.7689 (m-40) REVERT: B 182 SER cc_start: 0.8648 (m) cc_final: 0.8413 (t) REVERT: B 344 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8087 (tm-30) REVERT: B 506 GLU cc_start: 0.8887 (pt0) cc_final: 0.8519 (pt0) REVERT: B 556 LEU cc_start: 0.8703 (mt) cc_final: 0.8457 (tp) REVERT: C 12 LEU cc_start: 0.7898 (tp) cc_final: 0.7637 (tp) REVERT: C 228 MET cc_start: 0.8536 (ppp) cc_final: 0.7999 (tmm) outliers start: 23 outliers final: 13 residues processed: 158 average time/residue: 0.1000 time to fit residues: 23.8294 Evaluate side-chains 163 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 97 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 15 optimal weight: 0.0270 chunk 79 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 HIS ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** 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 = 0.4333 r_free = 0.4333 target = 0.178327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.129484 restraints weight = 22961.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.127913 restraints weight = 14547.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.129120 restraints weight = 12962.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.128721 restraints weight = 10204.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.129079 restraints weight = 9394.602| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12005 Z= 0.137 Angle : 0.655 14.019 16137 Z= 0.334 Chirality : 0.043 0.178 1825 Planarity : 0.003 0.058 2043 Dihedral : 4.427 23.080 1534 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.22 % Favored : 95.57 % Rotamer: Outliers : 1.62 % Allowed : 17.06 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.23 (0.23), residues: 1422 helix: 2.02 (0.18), residues: 806 sheet: -0.24 (0.42), residues: 145 loop : -0.98 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 194 TYR 0.028 0.002 TYR C 150 PHE 0.029 0.002 PHE C 30 TRP 0.012 0.001 TRP C 98 HIS 0.007 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00310 (12005) covalent geometry : angle 0.65482 (16137) hydrogen bonds : bond 0.03951 ( 728) hydrogen bonds : angle 4.29434 ( 2118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2248.03 seconds wall clock time: 39 minutes 49.79 seconds (2389.79 seconds total)