Starting phenix.real_space_refine on Thu Jul 2 15:03:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8qsk_18634/07_2026/8qsk_18634.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsk_18634/07_2026/8qsk_18634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qsk_18634/07_2026/8qsk_18634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsk_18634/07_2026/8qsk_18634.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8qsk_18634/07_2026/8qsk_18634.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8qsk_18634/07_2026/8qsk_18634.cif" model { file = "/net/cci-nas-00/data/ceres_data/8qsk_18634/07_2026/8qsk_18634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsk_18634/07_2026/8qsk_18634.cif" } resolution = 3.3 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= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 48 5.16 5 C 5702 2.51 5 N 1310 2.21 5 O 1444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8506 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 23, 'TRANS': 499} Chain breaks: 1 Chain: "C" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 23, 'TRANS': 499} Chain breaks: 1 Chain: "A" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'NAG': 1, 'PGT': 1, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'NAG': 1, 'PGT': 1, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.73, per 1000 atoms: 0.20 Number of scatterers: 8506 At special positions: 0 Unit cell: (126.445, 76.285, 87.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 2 15.00 O 1444 8.00 N 1310 7.00 C 5702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 153 " 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=0, symmetry=0 Links applied NAG-ASN " NAG A 603 " - " ASN A 140 " " NAG C 604 " - " ASN C 140 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 190.3 milliseconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 2 sheets defined 81.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 removed outlier: 3.541A pdb=" N ALA A 20 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 57 removed outlier: 3.639A pdb=" N CYS A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 70 through 98 removed outlier: 3.943A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 101 through 118 Processing helix chain 'A' and resid 118 through 125 removed outlier: 3.846A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 153 through 183 removed outlier: 4.480A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.660A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 220 removed outlier: 3.531A pdb=" N THR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 248 removed outlier: 3.686A pdb=" N ALA A 227 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 4.155A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 273 removed outlier: 3.681A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 removed outlier: 4.236A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 348 Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix removed outlier: 3.874A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 367 through 395 removed outlier: 4.525A pdb=" N ASP A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) Proline residue: A 382 - end of helix removed outlier: 4.612A pdb=" N ASP A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Proline residue: A 390 - end of helix removed outlier: 4.114A pdb=" N HIS A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 430 removed outlier: 3.912A pdb=" N ARG A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 removed outlier: 3.512A pdb=" N TRP A 453 " --> pdb=" O SER A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 454 through 479 removed outlier: 3.516A pdb=" N TYR A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 511 Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 531 through 560 removed outlier: 4.009A pdb=" N TYR A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 28 removed outlier: 3.670A pdb=" N ALA C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 57 removed outlier: 3.649A pdb=" N CYS C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 70 through 98 removed outlier: 3.930A pdb=" N SER C 89 " --> pdb=" O THR C 85 " (cutoff:3.500A) Proline residue: C 90 - end of helix Processing helix chain 'C' and resid 101 through 118 Processing helix chain 'C' and resid 118 through 125 removed outlier: 3.869A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 153 through 183 removed outlier: 4.510A pdb=" N THR C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) Proline residue: C 177 - end of helix removed outlier: 3.701A pdb=" N VAL C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 220 removed outlier: 3.517A pdb=" N THR C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 248 removed outlier: 3.697A pdb=" N ALA C 227 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE C 228 " --> pdb=" O THR C 224 " (cutoff:3.500A) Proline residue: C 229 - end of helix removed outlier: 4.153A pdb=" N SER C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL C 246 " --> pdb=" O CYS C 242 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 273 removed outlier: 3.892A pdb=" N MET C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 303 Processing helix chain 'C' and resid 308 through 348 Proline residue: C 323 - end of helix Proline residue: C 330 - end of helix removed outlier: 3.848A pdb=" N VAL C 343 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 Processing helix chain 'C' and resid 367 through 395 removed outlier: 4.512A pdb=" N ASP C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA C 374 " --> pdb=" O THR C 370 " (cutoff:3.500A) Proline residue: C 382 - end of helix removed outlier: 4.615A pdb=" N ASP C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Proline residue: C 390 - end of helix removed outlier: 4.112A pdb=" N HIS C 395 " --> pdb=" O ILE C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 430 removed outlier: 3.947A pdb=" N ARG C 404 " --> pdb=" O SER C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 453 removed outlier: 3.518A pdb=" N TRP C 453 " --> pdb=" O SER C 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 450 through 453' Processing helix chain 'C' and resid 454 through 479 removed outlier: 3.503A pdb=" N TYR C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C 471 " --> pdb=" O PHE C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 511 Processing helix chain 'C' and resid 526 through 530 Processing helix chain 'C' and resid 532 through 560 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA2, first strand: chain 'C' and resid 435 through 436 592 hydrogen bonds defined for protein. 1746 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: 1.01 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1253 1.32 - 1.44: 2341 1.44 - 1.56: 5074 1.56 - 1.69: 4 1.69 - 1.81: 70 Bond restraints: 8742 Sorted by residual: bond pdb=" N HIS C 303 " pdb=" CA HIS C 303 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.51e+00 bond pdb=" N THR C 308 " pdb=" CA THR C 308 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.90e+00 bond pdb=" N THR A 308 " pdb=" CA THR A 308 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.88e+00 bond pdb=" N ILE A 421 " pdb=" CA ILE A 421 " ideal model delta sigma weight residual 1.461 1.492 -0.030 1.17e-02 7.31e+03 6.75e+00 bond pdb=" N ILE C 421 " pdb=" CA ILE C 421 " ideal model delta sigma weight residual 1.461 1.492 -0.030 1.17e-02 7.31e+03 6.75e+00 ... (remaining 8737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 11427 1.35 - 2.70: 376 2.70 - 4.05: 94 4.05 - 5.41: 31 5.41 - 6.76: 4 Bond angle restraints: 11932 Sorted by residual: angle pdb=" N LEU C 429 " pdb=" CA LEU C 429 " pdb=" C LEU C 429 " ideal model delta sigma weight residual 113.18 108.36 4.82 1.21e+00 6.83e-01 1.59e+01 angle pdb=" N LEU A 429 " pdb=" CA LEU A 429 " pdb=" C LEU A 429 " ideal model delta sigma weight residual 113.18 108.42 4.76 1.21e+00 6.83e-01 1.55e+01 angle pdb=" N ASN A 428 " pdb=" CA ASN A 428 " pdb=" C ASN A 428 " ideal model delta sigma weight residual 113.88 109.04 4.84 1.23e+00 6.61e-01 1.55e+01 angle pdb=" N ASN C 428 " pdb=" CA ASN C 428 " pdb=" C ASN C 428 " ideal model delta sigma weight residual 113.88 109.07 4.81 1.23e+00 6.61e-01 1.53e+01 angle pdb=" CA GLY A 305 " pdb=" C GLY A 305 " pdb=" O GLY A 305 " ideal model delta sigma weight residual 122.46 118.70 3.76 9.70e-01 1.06e+00 1.50e+01 ... (remaining 11927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4580 17.34 - 34.68: 296 34.68 - 52.02: 61 52.02 - 69.36: 26 69.36 - 86.70: 3 Dihedral angle restraints: 4966 sinusoidal: 1974 harmonic: 2992 Sorted by residual: dihedral pdb=" CA LEU C 397 " pdb=" C LEU C 397 " pdb=" N LEU C 398 " pdb=" CA LEU C 398 " ideal model delta harmonic sigma weight residual -180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA LEU A 397 " pdb=" C LEU A 397 " pdb=" N LEU A 398 " pdb=" CA LEU A 398 " ideal model delta harmonic sigma weight residual -180.00 -161.45 -18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA GLY A 396 " pdb=" C GLY A 396 " pdb=" N LEU A 397 " pdb=" CA LEU A 397 " ideal model delta harmonic sigma weight residual -180.00 -162.72 -17.28 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 4963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1042 0.037 - 0.073: 245 0.073 - 0.109: 86 0.109 - 0.146: 13 0.146 - 0.182: 12 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CB VAL A 430 " pdb=" CA VAL A 430 " pdb=" CG1 VAL A 430 " pdb=" CG2 VAL A 430 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.33e-01 chirality pdb=" CA ILE C 421 " pdb=" N ILE C 421 " pdb=" C ILE C 421 " pdb=" CB ILE C 421 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CB VAL C 430 " pdb=" CA VAL C 430 " pdb=" CG1 VAL C 430 " pdb=" CG2 VAL C 430 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 1395 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 426 " -0.401 9.50e-02 1.11e+02 1.80e-01 1.99e+01 pdb=" NE ARG C 426 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG C 426 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 426 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 426 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 426 " 0.344 9.50e-02 1.11e+02 1.54e-01 1.47e+01 pdb=" NE ARG A 426 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 426 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 426 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 426 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 462 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.61e+00 pdb=" C GLY C 462 " -0.028 2.00e-02 2.50e+03 pdb=" O GLY C 462 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE C 463 " 0.009 2.00e-02 2.50e+03 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1490 2.77 - 3.30: 9050 3.30 - 3.83: 14177 3.83 - 4.37: 16095 4.37 - 4.90: 27384 Nonbonded interactions: 68196 Sorted by model distance: nonbonded pdb=" O LEU A 264 " pdb=" OG SER A 267 " model vdw 2.235 3.040 nonbonded pdb=" O LEU A 122 " pdb=" OG1 THR A 128 " model vdw 2.254 3.040 nonbonded pdb=" O LEU C 122 " pdb=" OG1 THR C 128 " model vdw 2.257 3.040 nonbonded pdb=" O ILE A 461 " pdb=" OG SER A 464 " model vdw 2.261 3.040 nonbonded pdb=" O LYS A 262 " pdb=" OG1 THR A 265 " model vdw 2.265 3.040 ... (remaining 68191 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 16 through 602 or resid 605 through 606)) selection = (chain 'C' and (resid 16 through 602 or resid 605 through 606)) } 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: 1.180 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.650 Find NCS groups from input model: 0.140 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 0.035 8748 Z= 0.209 Angle : 0.631 6.757 11946 Z= 0.368 Chirality : 0.040 0.182 1398 Planarity : 0.008 0.180 1410 Dihedral : 12.566 86.701 3038 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.94 % Favored : 92.87 % Rotamer: Outliers : 1.59 % Allowed : 8.90 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.79 (0.28), residues: 1038 helix: 2.22 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -2.00 (0.42), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 426 TYR 0.008 0.001 TYR A 458 PHE 0.010 0.001 PHE A 67 TRP 0.005 0.001 TRP A 197 HIS 0.001 0.000 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.21 ( 8742) covalent geometry : angle 0.62998 / 0.37 (11932) SS BOND : bond 0.00055 / 0.03 ( 4) SS BOND : angle 0.33645 / 0.21 ( 8) hydrogen bonds : bond 0.10809 / 7.48 ( 592) hydrogen bonds : angle 5.09535 / 3.69 ( 1746) link_NAG-ASN : bond 0.00362 / 0.21 ( 2) link_NAG-ASN : angle 2.06753 / 1.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 221 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ILE cc_start: 0.8484 (mm) cc_final: 0.7688 (mm) REVERT: A 185 ASP cc_start: 0.8443 (m-30) cc_final: 0.8090 (m-30) REVERT: A 343 VAL cc_start: 0.8969 (t) cc_final: 0.8755 (m) REVERT: C 269 CYS cc_start: 0.9218 (m) cc_final: 0.8959 (t) outliers start: 13 outliers final: 6 residues processed: 229 average time/residue: 0.0716 time to fit residues: 23.7175 Evaluate side-chains 108 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain C residue 395 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.0470 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.129500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.105284 restraints weight = 18596.404| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.27 r_work: 0.3518 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 8748 Z= 0.144 Angle : 0.667 15.441 11946 Z= 0.319 Chirality : 0.040 0.188 1398 Planarity : 0.005 0.034 1410 Dihedral : 9.705 59.845 1350 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.88 % Allowed : 14.02 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.28), residues: 1038 helix: 2.33 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -1.96 (0.44), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 19 TYR 0.009 0.001 TYR A 534 PHE 0.020 0.001 PHE A 198 TRP 0.010 0.001 TRP A 69 HIS 0.003 0.001 HIS A 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 8742) covalent geometry : angle 0.66516 / 0.32 (11932) SS BOND : bond 0.00068 / 0.04 ( 4) SS BOND : angle 0.38379 / 0.25 ( 8) hydrogen bonds : bond 0.04207 / 2.76 ( 592) hydrogen bonds : angle 4.09213 / 2.95 ( 1746) link_NAG-ASN : bond 0.00233 / 0.14 ( 2) link_NAG-ASN : angle 2.26113 / 1.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8416 (mm) REVERT: A 266 TYR cc_start: 0.8974 (m-80) cc_final: 0.8625 (m-80) REVERT: A 343 VAL cc_start: 0.8972 (t) cc_final: 0.8741 (m) REVERT: A 546 THR cc_start: 0.8955 (m) cc_final: 0.8746 (p) REVERT: C 33 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6808 (ptp90) REVERT: C 91 PHE cc_start: 0.7604 (m-10) cc_final: 0.7395 (m-10) REVERT: C 208 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8432 (mm) REVERT: C 266 TYR cc_start: 0.8951 (m-80) cc_final: 0.8748 (m-80) REVERT: C 269 CYS cc_start: 0.9148 (m) cc_final: 0.8927 (t) REVERT: C 307 PHE cc_start: 0.8354 (m-80) cc_final: 0.7964 (m-10) outliers start: 40 outliers final: 19 residues processed: 133 average time/residue: 0.0621 time to fit residues: 12.7958 Evaluate side-chains 110 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 554 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 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 = 0.3969 r_free = 0.3969 target = 0.124250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.099552 restraints weight = 18428.534| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.25 r_work: 0.3424 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8748 Z= 0.145 Angle : 0.614 6.709 11946 Z= 0.299 Chirality : 0.039 0.172 1398 Planarity : 0.004 0.031 1410 Dihedral : 9.582 59.444 1342 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.76 % Allowed : 15.49 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.28), residues: 1038 helix: 2.20 (0.18), residues: 782 sheet: None (None), residues: 0 loop : -1.89 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 186 TYR 0.009 0.001 TYR A 266 PHE 0.014 0.001 PHE A 198 TRP 0.007 0.001 TRP A 200 HIS 0.002 0.001 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 8742) covalent geometry : angle 0.61240 / 0.30 (11932) SS BOND : bond 0.00037 / 0.02 ( 4) SS BOND : angle 0.22842 / 0.13 ( 8) hydrogen bonds : bond 0.04034 / 2.64 ( 592) hydrogen bonds : angle 3.98413 / 2.91 ( 1746) link_NAG-ASN : bond 0.00280 / 0.17 ( 2) link_NAG-ASN : angle 2.16388 / 1.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7960 (m-10) cc_final: 0.7692 (m-10) REVERT: A 185 ASP cc_start: 0.8463 (m-30) cc_final: 0.8125 (t70) REVERT: A 208 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8452 (mm) REVERT: A 266 TYR cc_start: 0.8984 (m-80) cc_final: 0.8542 (m-80) REVERT: A 307 PHE cc_start: 0.8449 (m-80) cc_final: 0.7864 (m-10) REVERT: A 343 VAL cc_start: 0.9072 (t) cc_final: 0.8791 (m) REVERT: C 91 PHE cc_start: 0.7765 (m-10) cc_final: 0.7510 (m-10) REVERT: C 208 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8419 (mm) REVERT: C 266 TYR cc_start: 0.8906 (m-80) cc_final: 0.8580 (m-80) REVERT: C 269 CYS cc_start: 0.9220 (m) cc_final: 0.8916 (t) REVERT: C 307 PHE cc_start: 0.8316 (m-80) cc_final: 0.7999 (m-10) outliers start: 39 outliers final: 27 residues processed: 118 average time/residue: 0.0533 time to fit residues: 10.1056 Evaluate side-chains 105 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 554 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.0370 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.122722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.097840 restraints weight = 18899.614| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.30 r_work: 0.3404 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8748 Z= 0.121 Angle : 0.585 8.013 11946 Z= 0.279 Chirality : 0.038 0.147 1398 Planarity : 0.004 0.033 1410 Dihedral : 9.498 59.564 1342 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 4.76 % Allowed : 17.68 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.99 (0.28), residues: 1038 helix: 2.25 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -1.62 (0.46), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 186 TYR 0.007 0.001 TYR A 113 PHE 0.013 0.001 PHE A 198 TRP 0.004 0.001 TRP C 452 HIS 0.001 0.000 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 8742) covalent geometry : angle 0.58347 / 0.28 (11932) SS BOND : bond 0.00016 / 0.01 ( 4) SS BOND : angle 0.15960 / 0.09 ( 8) hydrogen bonds : bond 0.03765 / 2.48 ( 592) hydrogen bonds : angle 3.91485 / 2.84 ( 1746) link_NAG-ASN : bond 0.00284 / 0.17 ( 2) link_NAG-ASN : angle 2.06884 / 1.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 81 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7925 (m-10) cc_final: 0.7579 (m-10) REVERT: A 208 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8488 (mm) REVERT: A 266 TYR cc_start: 0.8864 (m-10) cc_final: 0.8447 (m-80) REVERT: A 307 PHE cc_start: 0.8510 (m-80) cc_final: 0.7752 (m-10) REVERT: C 208 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8494 (mm) REVERT: C 266 TYR cc_start: 0.8926 (m-10) cc_final: 0.8523 (m-80) REVERT: C 307 PHE cc_start: 0.8260 (m-80) cc_final: 0.7982 (m-10) outliers start: 39 outliers final: 28 residues processed: 110 average time/residue: 0.0494 time to fit residues: 8.9009 Evaluate side-chains 108 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 554 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 40 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 53 optimal weight: 0.0870 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.117997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093188 restraints weight = 18687.765| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.22 r_work: 0.3320 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8748 Z= 0.150 Angle : 0.600 7.798 11946 Z= 0.289 Chirality : 0.039 0.160 1398 Planarity : 0.004 0.033 1410 Dihedral : 9.352 59.870 1342 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.27 % Allowed : 19.39 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.89 (0.28), residues: 1038 helix: 2.19 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -1.71 (0.45), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 186 TYR 0.011 0.001 TYR C 52 PHE 0.013 0.001 PHE A 67 TRP 0.006 0.001 TRP C 368 HIS 0.001 0.001 HIS C 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 8742) covalent geometry : angle 0.59862 / 0.29 (11932) SS BOND : bond 0.00049 / 0.03 ( 4) SS BOND : angle 0.25669 / 0.14 ( 8) hydrogen bonds : bond 0.03923 / 2.58 ( 592) hydrogen bonds : angle 3.91326 / 2.87 ( 1746) link_NAG-ASN : bond 0.00315 / 0.19 ( 2) link_NAG-ASN : angle 1.98107 / 1.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8638 (mm) REVERT: A 266 TYR cc_start: 0.9076 (m-10) cc_final: 0.8533 (m-80) REVERT: A 307 PHE cc_start: 0.8513 (m-80) cc_final: 0.7920 (m-10) REVERT: C 208 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8587 (mm) REVERT: C 266 TYR cc_start: 0.8869 (m-10) cc_final: 0.8467 (m-80) REVERT: C 307 PHE cc_start: 0.8292 (m-80) cc_final: 0.7991 (m-10) outliers start: 35 outliers final: 27 residues processed: 109 average time/residue: 0.0538 time to fit residues: 9.3819 Evaluate side-chains 107 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 554 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 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 = 0.3864 r_free = 0.3864 target = 0.116673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.092082 restraints weight = 18614.803| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.12 r_work: 0.3304 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8748 Z= 0.138 Angle : 0.588 7.259 11946 Z= 0.281 Chirality : 0.038 0.146 1398 Planarity : 0.004 0.035 1410 Dihedral : 9.211 59.440 1342 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 4.27 % Allowed : 20.00 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.94 (0.28), residues: 1038 helix: 2.20 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -1.62 (0.45), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 186 TYR 0.009 0.001 TYR C 444 PHE 0.013 0.001 PHE A 67 TRP 0.005 0.001 TRP C 368 HIS 0.001 0.000 HIS C 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 8742) covalent geometry : angle 0.58625 / 0.28 (11932) SS BOND : bond 0.00024 / 0.01 ( 4) SS BOND : angle 0.17381 / 0.10 ( 8) hydrogen bonds : bond 0.03876 / 2.55 ( 592) hydrogen bonds : angle 3.92359 / 2.87 ( 1746) link_NAG-ASN : bond 0.00268 / 0.16 ( 2) link_NAG-ASN : angle 1.92475 / 1.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8628 (mm) REVERT: A 266 TYR cc_start: 0.9036 (m-10) cc_final: 0.8532 (m-80) REVERT: A 307 PHE cc_start: 0.8454 (m-80) cc_final: 0.7871 (m-10) REVERT: A 318 LEU cc_start: 0.8839 (mp) cc_final: 0.8564 (mp) REVERT: C 208 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8589 (mm) REVERT: C 266 TYR cc_start: 0.8918 (m-10) cc_final: 0.8531 (m-80) REVERT: C 307 PHE cc_start: 0.8302 (m-80) cc_final: 0.7975 (m-10) REVERT: C 318 LEU cc_start: 0.8863 (mp) cc_final: 0.8579 (mp) outliers start: 35 outliers final: 28 residues processed: 105 average time/residue: 0.0508 time to fit residues: 8.8610 Evaluate side-chains 102 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 554 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 88 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 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 = 0.3871 r_free = 0.3871 target = 0.117294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.092902 restraints weight = 18771.196| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.13 r_work: 0.3318 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8748 Z= 0.118 Angle : 0.584 8.328 11946 Z= 0.277 Chirality : 0.037 0.159 1398 Planarity : 0.004 0.029 1410 Dihedral : 8.925 59.329 1340 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.90 % Allowed : 20.61 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.28), residues: 1038 helix: 2.19 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -1.52 (0.45), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 186 TYR 0.007 0.001 TYR C 113 PHE 0.012 0.001 PHE C 198 TRP 0.004 0.001 TRP C 453 HIS 0.001 0.000 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 8742) covalent geometry : angle 0.58320 / 0.28 (11932) SS BOND : bond 0.00041 / 0.02 ( 4) SS BOND : angle 0.14890 / 0.08 ( 8) hydrogen bonds : bond 0.03704 / 2.45 ( 592) hydrogen bonds : angle 3.90252 / 2.85 ( 1746) link_NAG-ASN : bond 0.00369 / 0.22 ( 2) link_NAG-ASN : angle 1.66522 / 0.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8587 (mm) REVERT: A 266 TYR cc_start: 0.9042 (m-10) cc_final: 0.8560 (m-80) REVERT: A 307 PHE cc_start: 0.8454 (m-80) cc_final: 0.7865 (m-10) REVERT: A 318 LEU cc_start: 0.8871 (mp) cc_final: 0.8593 (mp) REVERT: C 208 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8579 (mm) REVERT: C 266 TYR cc_start: 0.8949 (m-10) cc_final: 0.8549 (m-80) REVERT: C 307 PHE cc_start: 0.8232 (m-80) cc_final: 0.7923 (m-10) REVERT: C 318 LEU cc_start: 0.8862 (mp) cc_final: 0.8581 (mp) outliers start: 32 outliers final: 26 residues processed: 107 average time/residue: 0.0535 time to fit residues: 9.2695 Evaluate side-chains 103 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 554 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 35 optimal weight: 0.0770 chunk 70 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 62 optimal weight: 0.3980 chunk 42 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.0020 chunk 36 optimal weight: 0.3980 chunk 28 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 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 = 0.3893 r_free = 0.3893 target = 0.118534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.094158 restraints weight = 18522.268| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.11 r_work: 0.3344 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8748 Z= 0.110 Angle : 0.584 9.772 11946 Z= 0.275 Chirality : 0.037 0.162 1398 Planarity : 0.004 0.033 1410 Dihedral : 8.687 59.588 1338 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.54 % Allowed : 21.46 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.05 (0.28), residues: 1038 helix: 2.20 (0.18), residues: 784 sheet: None (None), residues: 0 loop : -1.41 (0.46), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 104 TYR 0.007 0.001 TYR C 113 PHE 0.011 0.001 PHE C 198 TRP 0.004 0.001 TRP A 452 HIS 0.001 0.000 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 ( 8742) covalent geometry : angle 0.58373 / 0.27 (11932) SS BOND : bond 0.00046 / 0.03 ( 4) SS BOND : angle 0.14266 / 0.07 ( 8) hydrogen bonds : bond 0.03538 / 2.35 ( 592) hydrogen bonds : angle 3.87335 / 2.83 ( 1746) link_NAG-ASN : bond 0.00335 / 0.21 ( 2) link_NAG-ASN : angle 1.49132 / 0.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9117 (tt) cc_final: 0.8806 (tt) REVERT: A 208 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8552 (mm) REVERT: A 266 TYR cc_start: 0.9070 (m-10) cc_final: 0.8588 (m-80) REVERT: A 307 PHE cc_start: 0.8482 (m-80) cc_final: 0.7889 (m-10) REVERT: A 318 LEU cc_start: 0.8868 (mp) cc_final: 0.8612 (mp) REVERT: C 208 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8479 (mm) REVERT: C 266 TYR cc_start: 0.8979 (m-10) cc_final: 0.8555 (m-80) REVERT: C 307 PHE cc_start: 0.8230 (m-80) cc_final: 0.7922 (m-10) REVERT: C 318 LEU cc_start: 0.8900 (mp) cc_final: 0.8623 (mp) outliers start: 29 outliers final: 25 residues processed: 107 average time/residue: 0.0612 time to fit residues: 10.6789 Evaluate side-chains 105 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 443 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 73 optimal weight: 0.0040 chunk 80 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.117159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.092825 restraints weight = 18610.002| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.10 r_work: 0.3322 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8748 Z= 0.116 Angle : 0.596 8.523 11946 Z= 0.279 Chirality : 0.037 0.163 1398 Planarity : 0.004 0.028 1410 Dihedral : 8.573 59.594 1338 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.41 % Allowed : 22.32 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.07 (0.28), residues: 1038 helix: 2.21 (0.18), residues: 784 sheet: None (None), residues: 0 loop : -1.41 (0.46), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 186 TYR 0.007 0.001 TYR C 52 PHE 0.011 0.001 PHE A 67 TRP 0.006 0.001 TRP A 368 HIS 0.001 0.000 HIS C 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 8742) covalent geometry : angle 0.59592 / 0.28 (11932) SS BOND : bond 0.00041 / 0.02 ( 4) SS BOND : angle 0.14364 / 0.08 ( 8) hydrogen bonds : bond 0.03644 / 2.39 ( 592) hydrogen bonds : angle 3.84817 / 2.81 ( 1746) link_NAG-ASN : bond 0.00480 / 0.28 ( 2) link_NAG-ASN : angle 1.40787 / 0.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.223 Fit side-chains REVERT: A 95 LEU cc_start: 0.9115 (tt) cc_final: 0.8818 (tt) REVERT: A 208 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8581 (mm) REVERT: A 266 TYR cc_start: 0.9044 (m-10) cc_final: 0.8582 (m-80) REVERT: A 307 PHE cc_start: 0.8459 (m-80) cc_final: 0.7867 (m-10) REVERT: A 318 LEU cc_start: 0.8925 (mp) cc_final: 0.8633 (mp) REVERT: C 208 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8516 (mm) REVERT: C 266 TYR cc_start: 0.9016 (m-10) cc_final: 0.8586 (m-80) REVERT: C 307 PHE cc_start: 0.8274 (m-80) cc_final: 0.7961 (m-10) REVERT: C 318 LEU cc_start: 0.8910 (mp) cc_final: 0.8623 (mp) outliers start: 28 outliers final: 22 residues processed: 102 average time/residue: 0.0610 time to fit residues: 10.1134 Evaluate side-chains 98 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 443 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 75 optimal weight: 0.0770 chunk 39 optimal weight: 7.9990 chunk 73 optimal weight: 0.0270 chunk 2 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 52 optimal weight: 50.0000 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.116917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.092832 restraints weight = 18524.678| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.08 r_work: 0.3325 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8748 Z= 0.112 Angle : 0.593 8.739 11946 Z= 0.277 Chirality : 0.037 0.185 1398 Planarity : 0.004 0.032 1410 Dihedral : 8.501 59.796 1338 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.54 % Allowed : 22.56 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.09 (0.28), residues: 1038 helix: 2.23 (0.18), residues: 784 sheet: None (None), residues: 0 loop : -1.40 (0.45), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 186 TYR 0.008 0.001 TYR C 458 PHE 0.012 0.001 PHE C 198 TRP 0.004 0.001 TRP C 452 HIS 0.001 0.000 HIS A 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 8742) covalent geometry : angle 0.59253 / 0.28 (11932) SS BOND : bond 0.00017 / 0.01 ( 4) SS BOND : angle 0.15045 / 0.08 ( 8) hydrogen bonds : bond 0.03545 / 2.34 ( 592) hydrogen bonds : angle 3.84094 / 2.81 ( 1746) link_NAG-ASN : bond 0.00399 / 0.24 ( 2) link_NAG-ASN : angle 1.06043 / 0.59 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.324 Fit side-chains REVERT: A 95 LEU cc_start: 0.9110 (tt) cc_final: 0.8817 (tt) REVERT: A 208 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8597 (mm) REVERT: A 266 TYR cc_start: 0.9024 (m-10) cc_final: 0.8543 (m-80) REVERT: A 307 PHE cc_start: 0.8421 (m-80) cc_final: 0.7840 (m-10) REVERT: A 318 LEU cc_start: 0.8929 (mp) cc_final: 0.8637 (mp) REVERT: C 208 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8577 (mm) REVERT: C 266 TYR cc_start: 0.9038 (m-10) cc_final: 0.8593 (m-80) REVERT: C 307 PHE cc_start: 0.8253 (m-80) cc_final: 0.7940 (m-10) REVERT: C 318 LEU cc_start: 0.8909 (mp) cc_final: 0.8630 (mp) REVERT: C 339 GLN cc_start: 0.8700 (tt0) cc_final: 0.8462 (mt0) outliers start: 29 outliers final: 21 residues processed: 107 average time/residue: 0.0539 time to fit residues: 9.3921 Evaluate side-chains 102 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 443 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 72 optimal weight: 0.0870 chunk 26 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.115514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.091498 restraints weight = 18585.561| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.11 r_work: 0.3301 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8748 Z= 0.123 Angle : 0.604 8.308 11946 Z= 0.283 Chirality : 0.038 0.215 1398 Planarity : 0.004 0.028 1410 Dihedral : 8.414 59.765 1338 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.29 % Allowed : 22.68 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.28), residues: 1038 helix: 2.18 (0.18), residues: 784 sheet: None (None), residues: 0 loop : -1.34 (0.46), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 186 TYR 0.007 0.001 TYR C 52 PHE 0.012 0.001 PHE A 67 TRP 0.006 0.001 TRP A 368 HIS 0.001 0.000 HIS C 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 8742) covalent geometry : angle 0.60263 / 0.28 (11932) SS BOND : bond 0.00022 / 0.01 ( 4) SS BOND : angle 0.09500 / 0.06 ( 8) hydrogen bonds : bond 0.03707 / 2.44 ( 592) hydrogen bonds : angle 3.85828 / 2.82 ( 1746) link_NAG-ASN : bond 0.00124 / 0.08 ( 2) link_NAG-ASN : angle 1.74367 / 0.85 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1658.93 seconds wall clock time: 29 minutes 13.01 seconds (1753.01 seconds total)