Starting phenix.real_space_refine on Wed Aug 5 07:14:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/31ez_58354/08_2026/31ez_58354.cif Found real_map, /net/cci-nas-00/data/ceres_data/31ez_58354/08_2026/31ez_58354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/31ez_58354/08_2026/31ez_58354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/31ez_58354/08_2026/31ez_58354.map" model { file = "/net/cci-nas-00/data/ceres_data/31ez_58354/08_2026/31ez_58354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/31ez_58354/08_2026/31ez_58354.cif" } resolution = 3.48 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= 0.002 sd= 0.019 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 72 5.16 5 C 5862 2.51 5 N 1262 2.21 5 O 1452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8648 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3880 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 486} Chain: "B" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3880 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 486} Chain: "A" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 444 Unusual residues: {'ERG': 5, 'MYR': 18, 'XAN': 1} Classifications: {'undetermined': 24} Link IDs: {None: 23} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 444 Unusual residues: {'ERG': 5, 'MYR': 18, 'XAN': 1} Classifications: {'undetermined': 24} Link IDs: {None: 23} Time building chain proxies: 1.81, per 1000 atoms: 0.21 Number of scatterers: 8648 At special positions: 0 Unit cell: (122.82, 92.46, 80.04, 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 72 16.00 O 1452 8.00 N 1262 7.00 C 5862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 174 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS A 255 " distance=2.03 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 185 " distance=2.03 Simple disulfide: pdb=" SG CYS B 248 " - pdb=" SG CYS B 255 " distance=2.03 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 336.8 milliseconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1896 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 3 sheets defined 73.9% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 removed outlier: 3.631A pdb=" N HIS A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.664A pdb=" N PHE A 51 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 105 removed outlier: 4.448A pdb=" N ALA A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLY A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 108 through 133 removed outlier: 3.662A pdb=" N SER A 127 " --> pdb=" O CYS A 123 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N MET A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 172 removed outlier: 4.024A pdb=" N VAL A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.709A pdb=" N TYR A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 193 " --> pdb=" O TYR A 189 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 208 removed outlier: 3.522A pdb=" N ALA A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 219 through 241 Proline residue: A 225 - end of helix removed outlier: 3.608A pdb=" N LEU A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N THR A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 245 through 249 removed outlier: 3.758A pdb=" N CYS A 248 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N MET A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 245 through 249' Processing helix chain 'A' and resid 268 through 289 removed outlier: 3.774A pdb=" N VAL A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.893A pdb=" N SER A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 313 Processing helix chain 'A' and resid 317 through 322 removed outlier: 3.697A pdb=" N ALA A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 342 through 368 Processing helix chain 'A' and resid 374 through 397 Processing helix chain 'A' and resid 408 through 417 removed outlier: 3.648A pdb=" N VAL A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 437 removed outlier: 3.778A pdb=" N GLY A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 429 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 446 removed outlier: 3.827A pdb=" N ALA A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 472 removed outlier: 3.529A pdb=" N MET A 452 " --> pdb=" O PRO A 448 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 472 " --> pdb=" O GLN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 497 removed outlier: 3.941A pdb=" N LEU A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 removed outlier: 4.481A pdb=" N PHE A 501 " --> pdb=" O PRO A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 526 removed outlier: 3.989A pdb=" N GLU A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 540 removed outlier: 3.546A pdb=" N VAL A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 37 removed outlier: 3.708A pdb=" N HIS B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.675A pdb=" N PHE B 51 " --> pdb=" O TYR B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 105 removed outlier: 4.419A pdb=" N ALA B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLY B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Proline residue: B 97 - end of helix Processing helix chain 'B' and resid 108 through 133 removed outlier: 3.666A pdb=" N SER B 127 " --> pdb=" O CYS B 123 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG B 133 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 172 removed outlier: 4.070A pdb=" N VAL B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 removed outlier: 3.676A pdb=" N TYR B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 193 " --> pdb=" O TYR B 189 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS B 198 " --> pdb=" O GLY B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 removed outlier: 3.522A pdb=" N ALA B 207 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 219 through 241 Proline residue: B 225 - end of helix removed outlier: 3.589A pdb=" N LEU B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 245 through 249 removed outlier: 3.747A pdb=" N CYS B 248 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET B 249 " --> pdb=" O SER B 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 249' Processing helix chain 'B' and resid 268 through 289 removed outlier: 3.805A pdb=" N VAL B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.880A pdb=" N SER B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 313 Processing helix chain 'B' and resid 317 through 322 removed outlier: 3.678A pdb=" N ALA B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 368 removed outlier: 3.616A pdb=" N ILE B 346 " --> pdb=" O MET B 342 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 397 Processing helix chain 'B' and resid 407 through 417 removed outlier: 4.293A pdb=" N GLY B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 437 removed outlier: 3.786A pdb=" N GLY B 424 " --> pdb=" O ASN B 420 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 429 " --> pdb=" O TYR B 425 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 437 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 446 removed outlier: 3.828A pdb=" N ALA B 441 " --> pdb=" O PHE B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 472 removed outlier: 4.199A pdb=" N PHE B 458 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 471 " --> pdb=" O GLY B 467 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 472 " --> pdb=" O GLN B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 497 removed outlier: 3.885A pdb=" N LEU B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 502 removed outlier: 4.543A pdb=" N PHE B 501 " --> pdb=" O PRO B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 526 removed outlier: 3.976A pdb=" N GLU B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 540 removed outlier: 3.517A pdb=" N VAL B 530 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA2, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AA3, first strand: chain 'B' and resid 151 through 153 467 hydrogen bonds defined for protein. 1389 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: 1.10 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1932 1.33 - 1.45: 1598 1.45 - 1.57: 5192 1.57 - 1.70: 0 1.70 - 1.82: 106 Bond restraints: 8828 Sorted by residual: bond pdb=" CB GLU B 408 " pdb=" CG GLU B 408 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" C GLY B 244 " pdb=" N GLY B 245 " ideal model delta sigma weight residual 1.327 1.320 0.006 8.10e-03 1.52e+04 6.25e-01 bond pdb=" CB MET A 90 " pdb=" CG MET A 90 " ideal model delta sigma weight residual 1.520 1.497 0.023 3.00e-02 1.11e+03 5.80e-01 bond pdb=" CB MET A 542 " pdb=" CG MET A 542 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.66e-01 bond pdb=" CB MET B 542 " pdb=" CG MET B 542 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.41e-01 ... (remaining 8823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 11684 1.79 - 3.58: 178 3.58 - 5.36: 29 5.36 - 7.15: 5 7.15 - 8.94: 8 Bond angle restraints: 11904 Sorted by residual: angle pdb=" C ILE A 214 " pdb=" N GLN A 215 " pdb=" CA GLN A 215 " ideal model delta sigma weight residual 121.94 114.10 7.84 2.00e+00 2.50e-01 1.54e+01 angle pdb=" CB GLU B 408 " pdb=" CG GLU B 408 " pdb=" CD GLU B 408 " ideal model delta sigma weight residual 112.60 117.58 -4.98 1.70e+00 3.46e-01 8.58e+00 angle pdb=" N VAL A 222 " pdb=" CA VAL A 222 " pdb=" C VAL A 222 " ideal model delta sigma weight residual 111.81 109.41 2.40 8.60e-01 1.35e+00 7.81e+00 angle pdb=" C LEU B 254 " pdb=" N CYS B 255 " pdb=" CA CYS B 255 " ideal model delta sigma weight residual 122.38 114.34 8.04 2.90e+00 1.19e-01 7.69e+00 angle pdb=" C ILE B 214 " pdb=" N GLN B 215 " pdb=" CA GLN B 215 " ideal model delta sigma weight residual 121.94 116.55 5.39 2.00e+00 2.50e-01 7.27e+00 ... (remaining 11899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5176 17.79 - 35.57: 486 35.57 - 53.36: 122 53.36 - 71.15: 20 71.15 - 88.93: 6 Dihedral angle restraints: 5810 sinusoidal: 2852 harmonic: 2958 Sorted by residual: dihedral pdb=" CB CYS B 248 " pdb=" SG CYS B 248 " pdb=" SG CYS B 255 " pdb=" CB CYS B 255 " ideal model delta sinusoidal sigma weight residual -86.00 -145.59 59.59 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS A 248 " pdb=" SG CYS A 248 " pdb=" SG CYS A 255 " pdb=" CB CYS A 255 " ideal model delta sinusoidal sigma weight residual -86.00 -144.15 58.15 1 1.00e+01 1.00e-02 4.53e+01 dihedral pdb=" CA ASN A 410 " pdb=" CB ASN A 410 " pdb=" CG ASN A 410 " pdb=" OD1 ASN A 410 " ideal model delta sinusoidal sigma weight residual 120.00 -175.44 -64.56 2 2.00e+01 2.50e-03 9.79e+00 ... (remaining 5807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 936 0.034 - 0.068: 336 0.068 - 0.102: 75 0.102 - 0.136: 20 0.136 - 0.170: 3 Chirality restraints: 1370 Sorted by residual: chirality pdb=" CA LEU A 344 " pdb=" N LEU A 344 " pdb=" C LEU A 344 " pdb=" CB LEU A 344 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CG LEU B 484 " pdb=" CB LEU B 484 " pdb=" CD1 LEU B 484 " pdb=" CD2 LEU B 484 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA VAL A 209 " pdb=" N VAL A 209 " pdb=" C VAL A 209 " pdb=" CB VAL A 209 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1367 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 250 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" CG ASP A 250 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP A 250 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP A 250 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 264 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 265 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 264 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO B 265 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 265 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 265 " -0.019 5.00e-02 4.00e+02 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 5052 3.03 - 3.50: 8585 3.50 - 3.97: 13107 3.97 - 4.43: 15244 4.43 - 4.90: 23122 Nonbonded interactions: 65110 Sorted by model distance: nonbonded pdb=" N GLU B 408 " pdb=" OE1 GLU B 408 " model vdw 2.565 3.120 nonbonded pdb=" OD1 ASP A 250 " pdb=" N ASP A 251 " model vdw 2.587 3.120 nonbonded pdb=" O ILE A 214 " pdb=" CA GLN A 215 " model vdw 2.594 2.776 nonbonded pdb=" O THR A 499 " pdb=" OG1 THR A 499 " model vdw 2.600 3.040 nonbonded pdb=" O THR B 499 " pdb=" OG1 THR B 499 " model vdw 2.602 3.040 ... (remaining 65105 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 1006 or resid 1009 through 1011 or resid 1014 t \ hrough 1018 or resid 1020 through 1021 or resid 1023 through 1024)) selection = (chain 'B' and (resid 26 through 606 or resid 609 through 611 or resid 614 throu \ gh 618 or resid 620 through 621 or resid 623 through 624)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.600 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.003 0.039 8836 Z= 0.121 Angle : 0.594 8.939 11912 Z= 0.312 Chirality : 0.038 0.170 1370 Planarity : 0.004 0.035 1416 Dihedral : 14.227 88.931 3902 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.16 % Allowed : 22.24 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.26), residues: 1036 helix: 1.50 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.30 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.011 0.001 TYR A 492 PHE 0.008 0.001 PHE B 501 TRP 0.011 0.001 TRP A 266 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 8828) covalent geometry : angle 0.59310 / 0.31 (11904) SS BOND : bond 0.00136 / 0.07 ( 4) SS BOND : angle 1.64710 / 0.95 ( 8) hydrogen bonds : bond 0.17838 / 11.96 ( 467) hydrogen bonds : angle 5.54444 / 4.11 ( 1389) Misc. bond : bond 0.00177 / 0.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 MET cc_start: 0.8441 (mmm) cc_final: 0.8171 (mtp) REVERT: A 429 LEU cc_start: 0.9023 (mt) cc_final: 0.8610 (tt) REVERT: A 455 MET cc_start: 0.9283 (ttp) cc_final: 0.8974 (tmm) REVERT: B 126 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8795 (mm) REVERT: B 151 MET cc_start: 0.8447 (mmm) cc_final: 0.8176 (mmm) REVERT: B 187 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8621 (pm20) REVERT: B 342 MET cc_start: 0.8712 (tpp) cc_final: 0.8257 (mmm) REVERT: B 525 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8098 (mp0) outliers start: 18 outliers final: 13 residues processed: 80 average time/residue: 0.0736 time to fit residues: 8.9639 Evaluate side-chains 81 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 525 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.0670 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 181 ASN A 391 ASN A 410 ASN A 468 GLN A 507 GLN B 85 GLN B 167 GLN B 181 ASN B 391 ASN B 410 ASN B 507 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.102243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.084192 restraints weight = 23498.348| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.70 r_work: 0.3173 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8836 Z= 0.107 Angle : 0.490 7.784 11912 Z= 0.242 Chirality : 0.036 0.130 1370 Planarity : 0.004 0.040 1416 Dihedral : 7.277 54.753 2233 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.49 % Allowed : 19.71 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.36 (0.26), residues: 1036 helix: 1.60 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -0.47 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 133 TYR 0.010 0.001 TYR A 492 PHE 0.006 0.001 PHE A 134 TRP 0.005 0.001 TRP A 242 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 8828) covalent geometry : angle 0.48889 / 0.24 (11904) SS BOND : bond 0.00125 / 0.06 ( 4) SS BOND : angle 1.25719 / 0.73 ( 8) hydrogen bonds : bond 0.04368 / 2.99 ( 467) hydrogen bonds : angle 4.02179 / 2.99 ( 1389) Misc. bond : bond 0.00105 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8177 (tm-30) REVERT: A 429 LEU cc_start: 0.9045 (mt) cc_final: 0.8665 (tt) REVERT: A 455 MET cc_start: 0.9273 (ttp) cc_final: 0.8982 (tmm) REVERT: B 126 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8886 (mm) REVERT: B 130 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8333 (tm-30) REVERT: B 215 GLN cc_start: 0.9065 (mt0) cc_final: 0.8759 (mp10) REVERT: B 342 MET cc_start: 0.8414 (tpp) cc_final: 0.8070 (mmm) REVERT: B 405 THR cc_start: 0.9447 (OUTLIER) cc_final: 0.9217 (m) outliers start: 29 outliers final: 15 residues processed: 106 average time/residue: 0.0748 time to fit residues: 12.0008 Evaluate side-chains 87 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 452 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 94 optimal weight: 0.2980 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 100 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.101748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.083511 restraints weight = 23680.172| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.70 r_work: 0.3170 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8836 Z= 0.103 Angle : 0.487 8.002 11912 Z= 0.240 Chirality : 0.036 0.131 1370 Planarity : 0.004 0.046 1416 Dihedral : 6.721 59.131 2210 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.61 % Allowed : 18.15 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.44 (0.26), residues: 1036 helix: 1.67 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.44 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 380 TYR 0.007 0.001 TYR A 492 PHE 0.017 0.001 PHE B 276 TRP 0.006 0.001 TRP A 242 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 8828) covalent geometry : angle 0.48607 / 0.24 (11904) SS BOND : bond 0.00125 / 0.06 ( 4) SS BOND : angle 1.08544 / 0.64 ( 8) hydrogen bonds : bond 0.03952 / 2.73 ( 467) hydrogen bonds : angle 3.84816 / 2.86 ( 1389) Misc. bond : bond 0.00095 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.283 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: symmetry clash REVERT: A 429 LEU cc_start: 0.9060 (mt) cc_final: 0.8654 (tt) REVERT: A 455 MET cc_start: 0.9250 (ttp) cc_final: 0.8919 (tmm) REVERT: B 126 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8827 (mm) REVERT: B 342 MET cc_start: 0.8308 (tpp) cc_final: 0.8076 (mmm) REVERT: B 356 GLU cc_start: 0.8869 (tp30) cc_final: 0.8625 (tp30) REVERT: B 378 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8755 (mt-10) outliers start: 30 outliers final: 22 residues processed: 101 average time/residue: 0.0703 time to fit residues: 10.4873 Evaluate side-chains 91 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 452 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.101809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.083571 restraints weight = 24224.212| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.68 r_work: 0.3173 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8836 Z= 0.102 Angle : 0.478 6.445 11912 Z= 0.236 Chirality : 0.036 0.130 1370 Planarity : 0.004 0.047 1416 Dihedral : 6.583 59.305 2210 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 4.21 % Allowed : 17.67 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.56 (0.26), residues: 1036 helix: 1.78 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.44 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 33 TYR 0.006 0.001 TYR A 492 PHE 0.014 0.001 PHE B 276 TRP 0.006 0.001 TRP B 242 HIS 0.003 0.001 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 8828) covalent geometry : angle 0.47760 / 0.24 (11904) SS BOND : bond 0.00077 / 0.04 ( 4) SS BOND : angle 0.95257 / 0.56 ( 8) hydrogen bonds : bond 0.03713 / 2.56 ( 467) hydrogen bonds : angle 3.73127 / 2.77 ( 1389) Misc. bond : bond 0.00096 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 80 time to evaluate : 0.220 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 429 LEU cc_start: 0.9068 (mt) cc_final: 0.8733 (tt) REVERT: A 455 MET cc_start: 0.9242 (ttp) cc_final: 0.8881 (tmm) REVERT: A 462 SER cc_start: 0.9583 (OUTLIER) cc_final: 0.8802 (p) REVERT: B 356 GLU cc_start: 0.8845 (tp30) cc_final: 0.8619 (tp30) REVERT: B 378 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8666 (mt-10) outliers start: 35 outliers final: 27 residues processed: 105 average time/residue: 0.0708 time to fit residues: 11.1162 Evaluate side-chains 101 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 471 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.0030 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.098619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080500 restraints weight = 24348.795| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.65 r_work: 0.3116 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8836 Z= 0.152 Angle : 0.521 6.720 11912 Z= 0.257 Chirality : 0.037 0.132 1370 Planarity : 0.004 0.047 1416 Dihedral : 6.881 59.207 2208 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 4.69 % Allowed : 18.15 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.58 (0.26), residues: 1036 helix: 1.79 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -0.43 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 133 TYR 0.008 0.001 TYR A 45 PHE 0.010 0.001 PHE B 276 TRP 0.010 0.001 TRP A 242 HIS 0.003 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 8828) covalent geometry : angle 0.52063 / 0.26 (11904) SS BOND : bond 0.00060 / 0.03 ( 4) SS BOND : angle 1.16185 / 0.69 ( 8) hydrogen bonds : bond 0.04220 / 2.92 ( 467) hydrogen bonds : angle 3.87844 / 2.87 ( 1389) Misc. bond : bond 0.00098 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 74 time to evaluate : 0.189 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 262 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8754 (ttt180) REVERT: A 429 LEU cc_start: 0.9125 (mt) cc_final: 0.8699 (tt) REVERT: A 455 MET cc_start: 0.9176 (ttp) cc_final: 0.8821 (tmm) REVERT: A 462 SER cc_start: 0.9529 (OUTLIER) cc_final: 0.8706 (p) REVERT: B 168 MET cc_start: 0.8807 (tpp) cc_final: 0.8564 (tpp) REVERT: B 262 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8567 (ttt180) REVERT: B 344 LEU cc_start: 0.9172 (mm) cc_final: 0.8961 (mm) REVERT: B 378 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8687 (mt-10) REVERT: B 526 THR cc_start: 0.8839 (p) cc_final: 0.8593 (p) outliers start: 39 outliers final: 30 residues processed: 104 average time/residue: 0.0762 time to fit residues: 11.4179 Evaluate side-chains 103 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 471 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.099781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.081535 restraints weight = 23919.652| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.59 r_work: 0.3130 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8836 Z= 0.130 Angle : 0.507 6.446 11912 Z= 0.250 Chirality : 0.037 0.158 1370 Planarity : 0.004 0.048 1416 Dihedral : 6.833 59.771 2208 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 5.05 % Allowed : 19.23 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.52 (0.26), residues: 1036 helix: 1.76 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.48 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 133 TYR 0.007 0.001 TYR A 45 PHE 0.010 0.001 PHE B 276 TRP 0.008 0.001 TRP B 242 HIS 0.002 0.001 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 8828) covalent geometry : angle 0.50629 / 0.25 (11904) SS BOND : bond 0.00050 / 0.02 ( 4) SS BOND : angle 1.09996 / 0.65 ( 8) hydrogen bonds : bond 0.03970 / 2.75 ( 467) hydrogen bonds : angle 3.82227 / 2.83 ( 1389) Misc. bond : bond 0.00091 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 70 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8782 (mp10) REVERT: A 262 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8703 (ttt180) REVERT: A 360 ASP cc_start: 0.8442 (m-30) cc_final: 0.8199 (m-30) REVERT: A 382 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8833 (tm-30) REVERT: A 429 LEU cc_start: 0.9107 (mt) cc_final: 0.8696 (tt) REVERT: A 455 MET cc_start: 0.9149 (ttp) cc_final: 0.8774 (tmm) REVERT: A 462 SER cc_start: 0.9540 (OUTLIER) cc_final: 0.8697 (p) REVERT: B 262 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8580 (ttt180) REVERT: B 344 LEU cc_start: 0.9170 (mm) cc_final: 0.8953 (mm) REVERT: B 378 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8725 (mt-10) outliers start: 42 outliers final: 31 residues processed: 104 average time/residue: 0.0702 time to fit residues: 10.6767 Evaluate side-chains 100 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 64 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 471 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 12 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 68 optimal weight: 0.0970 chunk 101 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.100967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.082483 restraints weight = 23977.270| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.64 r_work: 0.3152 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8836 Z= 0.102 Angle : 0.512 6.860 11912 Z= 0.248 Chirality : 0.037 0.161 1370 Planarity : 0.004 0.048 1416 Dihedral : 6.640 59.302 2208 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.09 % Allowed : 19.95 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.52 (0.26), residues: 1036 helix: 1.72 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -0.41 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 63 TYR 0.007 0.001 TYR B 169 PHE 0.010 0.001 PHE B 276 TRP 0.005 0.001 TRP B 422 HIS 0.002 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 8828) covalent geometry : angle 0.51207 / 0.25 (11904) SS BOND : bond 0.00049 / 0.02 ( 4) SS BOND : angle 0.94529 / 0.56 ( 8) hydrogen bonds : bond 0.03603 / 2.49 ( 467) hydrogen bonds : angle 3.69342 / 2.74 ( 1389) Misc. bond : bond 0.00087 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 71 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8861 (tpp) cc_final: 0.8574 (mmm) REVERT: A 215 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8825 (mp10) REVERT: A 262 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8773 (ttt180) REVERT: A 429 LEU cc_start: 0.9080 (mt) cc_final: 0.8686 (tt) REVERT: A 455 MET cc_start: 0.9097 (ttp) cc_final: 0.8698 (tmm) REVERT: B 378 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8686 (mt-10) outliers start: 34 outliers final: 29 residues processed: 97 average time/residue: 0.0735 time to fit residues: 10.5317 Evaluate side-chains 94 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 471 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 6 optimal weight: 0.0670 chunk 8 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.101030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.082672 restraints weight = 23599.256| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.59 r_work: 0.3154 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8836 Z= 0.108 Angle : 0.522 7.626 11912 Z= 0.253 Chirality : 0.037 0.145 1370 Planarity : 0.004 0.048 1416 Dihedral : 6.589 59.465 2208 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.09 % Allowed : 20.67 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.54 (0.26), residues: 1036 helix: 1.81 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.53 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 133 TYR 0.006 0.001 TYR A 492 PHE 0.009 0.001 PHE B 276 TRP 0.006 0.001 TRP A 242 HIS 0.002 0.001 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 8828) covalent geometry : angle 0.52178 / 0.25 (11904) SS BOND : bond 0.00048 / 0.02 ( 4) SS BOND : angle 0.92250 / 0.55 ( 8) hydrogen bonds : bond 0.03594 / 2.48 ( 467) hydrogen bonds : angle 3.69056 / 2.74 ( 1389) Misc. bond : bond 0.00088 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 65 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8806 (mp10) REVERT: A 262 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8714 (ttt180) REVERT: A 429 LEU cc_start: 0.9078 (mt) cc_final: 0.8677 (tt) REVERT: A 455 MET cc_start: 0.9075 (ttp) cc_final: 0.8673 (tmm) REVERT: B 262 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8575 (ttt180) REVERT: B 378 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8676 (mt-10) outliers start: 34 outliers final: 26 residues processed: 93 average time/residue: 0.0698 time to fit residues: 9.4878 Evaluate side-chains 96 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 471 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 68 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.101540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.083305 restraints weight = 23619.837| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.60 r_work: 0.3164 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8836 Z= 0.102 Angle : 0.518 7.202 11912 Z= 0.251 Chirality : 0.037 0.138 1370 Planarity : 0.004 0.048 1416 Dihedral : 6.499 59.875 2208 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.61 % Allowed : 21.39 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.54 (0.26), residues: 1036 helix: 1.82 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.56 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 133 TYR 0.007 0.001 TYR B 169 PHE 0.010 0.001 PHE B 276 TRP 0.004 0.001 TRP A 242 HIS 0.002 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 8828) covalent geometry : angle 0.51783 / 0.25 (11904) SS BOND : bond 0.00058 / 0.03 ( 4) SS BOND : angle 0.81835 / 0.49 ( 8) hydrogen bonds : bond 0.03449 / 2.38 ( 467) hydrogen bonds : angle 3.63869 / 2.70 ( 1389) Misc. bond : bond 0.00080 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8800 (mp10) REVERT: A 262 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8723 (ttt180) REVERT: A 429 LEU cc_start: 0.9065 (mt) cc_final: 0.8673 (tt) REVERT: A 455 MET cc_start: 0.9084 (ttp) cc_final: 0.8694 (tmm) REVERT: B 262 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8573 (ttt180) REVERT: B 378 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8662 (mt-10) outliers start: 30 outliers final: 25 residues processed: 93 average time/residue: 0.0665 time to fit residues: 8.8975 Evaluate side-chains 93 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 471 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.100484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.082021 restraints weight = 23739.762| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.60 r_work: 0.3134 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8836 Z= 0.131 Angle : 0.537 7.929 11912 Z= 0.262 Chirality : 0.037 0.143 1370 Planarity : 0.004 0.047 1416 Dihedral : 6.692 59.950 2208 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.73 % Allowed : 21.27 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.51 (0.26), residues: 1036 helix: 1.79 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.57 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 63 TYR 0.009 0.001 TYR B 169 PHE 0.009 0.001 PHE B 276 TRP 0.008 0.001 TRP B 242 HIS 0.001 0.001 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 8828) covalent geometry : angle 0.53614 / 0.26 (11904) SS BOND : bond 0.00073 / 0.04 ( 4) SS BOND : angle 0.97179 / 0.58 ( 8) hydrogen bonds : bond 0.03829 / 2.64 ( 467) hydrogen bonds : angle 3.76696 / 2.78 ( 1389) Misc. bond : bond 0.00089 / 0.04 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8833 (mp10) REVERT: A 262 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8682 (ttt180) REVERT: A 403 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7920 (mmm) REVERT: A 429 LEU cc_start: 0.9092 (mt) cc_final: 0.8677 (tt) REVERT: A 455 MET cc_start: 0.9088 (ttp) cc_final: 0.8690 (tmm) REVERT: B 262 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8542 (ttt180) REVERT: B 378 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8681 (mt-10) outliers start: 31 outliers final: 26 residues processed: 92 average time/residue: 0.0672 time to fit residues: 8.8573 Evaluate side-chains 93 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 471 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 38 optimal weight: 0.7980 chunk 52 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.101989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.083530 restraints weight = 23567.853| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.60 r_work: 0.3162 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8836 Z= 0.107 Angle : 0.534 10.078 11912 Z= 0.257 Chirality : 0.037 0.130 1370 Planarity : 0.004 0.047 1416 Dihedral : 6.557 59.812 2208 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 3.73 % Allowed : 21.75 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.52 (0.26), residues: 1036 helix: 1.80 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.56 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 52 TYR 0.010 0.001 TYR B 169 PHE 0.009 0.001 PHE B 276 TRP 0.005 0.001 TRP A 242 HIS 0.002 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 8828) covalent geometry : angle 0.53405 / 0.26 (11904) SS BOND : bond 0.00050 / 0.02 ( 4) SS BOND : angle 0.84157 / 0.51 ( 8) hydrogen bonds : bond 0.03505 / 2.42 ( 467) hydrogen bonds : angle 3.66366 / 2.70 ( 1389) Misc. bond : bond 0.00075 / 0.04 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1367.90 seconds wall clock time: 24 minutes 14.86 seconds (1454.86 seconds total)