Starting phenix.real_space_refine on Sat Aug 23 02:45:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3j_36853/08_2025/8k3j_36853.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3j_36853/08_2025/8k3j_36853.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/8k3j_36853/08_2025/8k3j_36853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3j_36853/08_2025/8k3j_36853.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3j_36853/08_2025/8k3j_36853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3j_36853/08_2025/8k3j_36853.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= 0.000 sd= 0.038 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 42 5.16 5 C 5720 2.51 5 N 1576 2.21 5 O 1770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9108 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4448 Classifications: {'peptide': 574} Link IDs: {'PCIS': 5, 'PTRANS': 32, 'TRANS': 536} Chain: "B" Number of atoms: 4448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4448 Classifications: {'peptide': 574} Link IDs: {'PCIS': 5, 'PTRANS': 32, 'TRANS': 536} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.89, per 1000 atoms: 0.21 Number of scatterers: 9108 At special positions: 0 Unit cell: (144.44, 164.68, 103.96, 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 42 16.00 O 1770 8.00 N 1576 7.00 C 5720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 348 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 440 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 348 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 440 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 587 " 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1101 " - " ASN A 76 " " NAG A1102 " - " ASN A 477 " " NAG B1101 " - " ASN B 76 " " NAG B1102 " - " ASN B 477 " " NAG C 1 " - " ASN A 498 " " NAG D 1 " - " ASN A 461 " " NAG E 1 " - " ASN B 498 " " NAG F 1 " - " ASN B 461 " Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 245.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 36 sheets defined 3.7% alpha, 45.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 101 through 106 removed outlier: 4.250A pdb=" N ALA A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.521A pdb=" N GLU A 301 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 Processing helix chain 'B' and resid 101 through 106 removed outlier: 4.247A pdb=" N ALA B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.564A pdb=" N GLU B 301 " --> pdb=" O PHE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 582 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 41 removed outlier: 5.935A pdb=" N GLY A 36 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N SER A 66 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG A 62 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 49 removed outlier: 6.232A pdb=" N VAL A 46 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLY A 130 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE A 48 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N LEU A 132 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79 removed outlier: 3.597A pdb=" N THR A 78 " --> pdb=" O MET A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 59 removed outlier: 3.539A pdb=" N VAL A 57 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 144 through 146 removed outlier: 3.814A pdb=" N GLY A 203 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 144 through 146 removed outlier: 3.814A pdb=" N GLY A 203 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 218 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.843A pdb=" N ILE A 194 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 153 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 240 through 243 removed outlier: 6.599A pdb=" N PHE A 262 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 248 through 252 removed outlier: 6.201A pdb=" N THR A 249 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN A 324 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA A 251 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 257 through 260 Processing sheet with id=AB2, first strand: chain 'A' and resid 328 through 331 removed outlier: 6.545A pdb=" N ALA A 349 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 336 through 339 Processing sheet with id=AB4, first strand: chain 'A' and resid 344 through 347 Processing sheet with id=AB5, first strand: chain 'A' and resid 427 through 431 removed outlier: 3.601A pdb=" N SER A 504 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 436 through 438 Processing sheet with id=AB7, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.011A pdb=" N HIS A 531 " --> pdb=" O THR A 512 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 518 through 521 Processing sheet with id=AB9, first strand: chain 'A' and resid 526 through 528 Processing sheet with id=AC1, first strand: chain 'B' and resid 35 through 41 removed outlier: 5.953A pdb=" N GLY B 36 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N SER B 66 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG B 62 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.219A pdb=" N VAL B 46 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLY B 130 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE B 48 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N LEU B 132 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 78 through 79 removed outlier: 3.694A pdb=" N THR B 78 " --> pdb=" O MET B 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 56 through 59 removed outlier: 3.600A pdb=" N VAL B 57 " --> pdb=" O ILE B 97 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 144 through 146 removed outlier: 7.494A pdb=" N ALA B 145 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY B 203 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 144 through 146 removed outlier: 7.494A pdb=" N ALA B 145 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY B 203 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 218 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.835A pdb=" N ILE B 194 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 153 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 237 through 243 removed outlier: 5.661A pdb=" N ALA B 238 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ASN B 266 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE B 262 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 248 through 252 removed outlier: 6.007A pdb=" N THR B 249 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLN B 324 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA B 251 " --> pdb=" O GLN B 324 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 257 through 260 Processing sheet with id=AD2, first strand: chain 'B' and resid 328 through 331 removed outlier: 6.551A pdb=" N ALA B 349 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 336 through 339 Processing sheet with id=AD4, first strand: chain 'B' and resid 344 through 347 Processing sheet with id=AD5, first strand: chain 'B' and resid 427 through 431 removed outlier: 3.591A pdb=" N SER B 504 " --> pdb=" O ILE B 428 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 435 through 438 Processing sheet with id=AD7, first strand: chain 'B' and resid 510 through 513 removed outlier: 6.066A pdb=" N HIS B 531 " --> pdb=" O THR B 512 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 518 through 521 Processing sheet with id=AD9, first strand: chain 'B' and resid 526 through 528 332 hydrogen bonds defined for protein. 750 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: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2966 1.34 - 1.46: 1709 1.46 - 1.58: 4579 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 9314 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.541 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.510 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C5 MAN C 4 " pdb=" O5 MAN C 4 " ideal model delta sigma weight residual 1.418 1.463 -0.045 2.00e-02 2.50e+03 5.00e+00 ... (remaining 9309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 12440 2.16 - 4.33: 203 4.33 - 6.49: 23 6.49 - 8.66: 3 8.66 - 10.82: 3 Bond angle restraints: 12672 Sorted by residual: angle pdb=" C ASN A 498 " pdb=" CA ASN A 498 " pdb=" CB ASN A 498 " ideal model delta sigma weight residual 109.99 115.83 -5.84 1.61e+00 3.86e-01 1.32e+01 angle pdb=" CB MET B 152 " pdb=" CG MET B 152 " pdb=" SD MET B 152 " ideal model delta sigma weight residual 112.70 123.52 -10.82 3.00e+00 1.11e-01 1.30e+01 angle pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " pdb=" C5 NAG C 1 " ideal model delta sigma weight residual 113.21 123.65 -10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CB MET A 152 " pdb=" CG MET A 152 " pdb=" SD MET A 152 " ideal model delta sigma weight residual 112.70 122.62 -9.92 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CA ASN A 461 " pdb=" CB ASN A 461 " pdb=" CG ASN A 461 " ideal model delta sigma weight residual 112.60 115.36 -2.76 1.00e+00 1.00e+00 7.64e+00 ... (remaining 12667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.21: 5224 23.21 - 46.43: 480 46.43 - 69.64: 77 69.64 - 92.86: 41 92.86 - 116.07: 30 Dihedral angle restraints: 5852 sinusoidal: 2544 harmonic: 3308 Sorted by residual: dihedral pdb=" CB CYS A 348 " pdb=" SG CYS A 348 " pdb=" SG CYS A 395 " pdb=" CB CYS A 395 " ideal model delta sinusoidal sigma weight residual 93.00 176.17 -83.17 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS B 155 " pdb=" SG CYS B 155 " pdb=" SG CYS B 207 " pdb=" CB CYS B 207 " ideal model delta sinusoidal sigma weight residual -86.00 -3.16 -82.84 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS A 155 " pdb=" SG CYS A 155 " pdb=" SG CYS A 207 " pdb=" CB CYS A 207 " ideal model delta sinusoidal sigma weight residual -86.00 -3.73 -82.27 1 1.00e+01 1.00e-02 8.31e+01 ... (remaining 5849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1308 0.080 - 0.160: 145 0.160 - 0.240: 5 0.240 - 0.319: 2 0.319 - 0.399: 2 Chirality restraints: 1462 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 461 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 461 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1459 not shown) Planarity restraints: 1648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 461 " -0.023 2.00e-02 2.50e+03 2.26e-02 6.37e+00 pdb=" CG ASN A 461 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 461 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 461 " 0.028 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 498 " 0.020 2.00e-02 2.50e+03 2.02e-02 5.12e+00 pdb=" CG ASN A 498 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 498 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 498 " -0.010 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 83 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO B 84 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 84 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 84 " 0.026 5.00e-02 4.00e+02 ... (remaining 1645 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 257 2.69 - 3.24: 8050 3.24 - 3.80: 12984 3.80 - 4.35: 16991 4.35 - 4.90: 29008 Nonbonded interactions: 67290 Sorted by model distance: nonbonded pdb=" N GLN A 32 " pdb=" NE2 GLN A 32 " model vdw 2.138 3.200 nonbonded pdb=" NZ LYS A 144 " pdb=" O ALA A 145 " model vdw 2.223 3.120 nonbonded pdb=" NZ LYS B 144 " pdb=" O ALA B 145 " model vdw 2.245 3.120 nonbonded pdb=" OD1 ASN A 498 " pdb=" O6 NAG C 1 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASP A 535 " pdb=" OG1 THR A 537 " model vdw 2.277 3.040 ... (remaining 67285 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.610 Find NCS groups from input model: 0.090 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 9342 Z= 0.207 Angle : 0.724 10.824 12744 Z= 0.349 Chirality : 0.049 0.399 1462 Planarity : 0.004 0.047 1640 Dihedral : 20.459 116.072 3680 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.72 % Favored : 95.10 % Rotamer: Outliers : 0.31 % Allowed : 23.19 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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 aren not related in a simple way. whole: -0.34 (0.25), residues: 1144 helix: None (None), residues: 0 sheet: 0.82 (0.23), residues: 500 loop : -1.13 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 480 TYR 0.007 0.001 TYR B 405 PHE 0.008 0.001 PHE B 135 TRP 0.023 0.001 TRP A 149 HIS 0.003 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 9314) covalent geometry : angle 0.68726 (12672) SS BOND : bond 0.00191 ( 12) SS BOND : angle 0.76769 ( 24) hydrogen bonds : bond 0.14758 ( 318) hydrogen bonds : angle 6.16753 ( 750) link_ALPHA1-3 : bond 0.00846 ( 2) link_ALPHA1-3 : angle 1.52032 ( 6) link_BETA1-4 : bond 0.00851 ( 6) link_BETA1-4 : angle 3.29041 ( 18) link_NAG-ASN : bond 0.00947 ( 8) link_NAG-ASN : angle 4.47192 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.316 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 0.0662 time to fit residues: 5.5650 Evaluate side-chains 51 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.0270 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.0570 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.140382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.114123 restraints weight = 19555.551| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 4.71 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.0573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9342 Z= 0.113 Angle : 0.682 11.746 12744 Z= 0.318 Chirality : 0.049 0.364 1462 Planarity : 0.004 0.046 1640 Dihedral : 16.135 109.635 1575 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 2.80 % Allowed : 22.57 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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 aren not related in a simple way. whole: -0.42 (0.25), residues: 1144 helix: -3.11 (1.57), residues: 12 sheet: 0.79 (0.23), residues: 524 loop : -1.24 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 87 TYR 0.007 0.001 TYR B 405 PHE 0.007 0.001 PHE A 382 TRP 0.013 0.001 TRP B 149 HIS 0.003 0.000 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9314) covalent geometry : angle 0.65429 (12672) SS BOND : bond 0.00168 ( 12) SS BOND : angle 0.65602 ( 24) hydrogen bonds : bond 0.03063 ( 318) hydrogen bonds : angle 5.27552 ( 750) link_ALPHA1-3 : bond 0.02097 ( 2) link_ALPHA1-3 : angle 1.48255 ( 6) link_BETA1-4 : bond 0.01113 ( 6) link_BETA1-4 : angle 3.19676 ( 18) link_NAG-ASN : bond 0.00936 ( 8) link_NAG-ASN : angle 3.49490 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 56 time to evaluate : 0.213 Fit side-chains REVERT: A 544 TRP cc_start: 0.5558 (m100) cc_final: 0.5075 (m-10) outliers start: 27 outliers final: 15 residues processed: 81 average time/residue: 0.0541 time to fit residues: 7.1561 Evaluate side-chains 68 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 10.0000 chunk 39 optimal weight: 0.0040 chunk 59 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.135993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.101178 restraints weight = 19454.891| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.11 r_work: 0.3365 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9342 Z= 0.246 Angle : 0.807 11.505 12744 Z= 0.384 Chirality : 0.053 0.440 1462 Planarity : 0.005 0.059 1640 Dihedral : 13.958 109.793 1572 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.69 % Favored : 92.13 % Rotamer: Outliers : 4.76 % Allowed : 20.70 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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 aren not related in a simple way. whole: -0.68 (0.25), residues: 1144 helix: -3.86 (1.11), residues: 12 sheet: 0.76 (0.23), residues: 498 loop : -1.46 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 182 TYR 0.015 0.002 TYR A 161 PHE 0.014 0.002 PHE B 245 TRP 0.013 0.003 TRP A 149 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 9314) covalent geometry : angle 0.77883 (12672) SS BOND : bond 0.00325 ( 12) SS BOND : angle 1.09565 ( 24) hydrogen bonds : bond 0.03904 ( 318) hydrogen bonds : angle 5.60836 ( 750) link_ALPHA1-3 : bond 0.01876 ( 2) link_ALPHA1-3 : angle 1.98552 ( 6) link_BETA1-4 : bond 0.00917 ( 6) link_BETA1-4 : angle 3.57651 ( 18) link_NAG-ASN : bond 0.00554 ( 8) link_NAG-ASN : angle 3.71233 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 54 time to evaluate : 0.255 Fit side-chains REVERT: A 128 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7508 (ptp-110) REVERT: A 176 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.5423 (m-80) REVERT: B 128 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7596 (mtm180) REVERT: B 135 PHE cc_start: 0.4799 (OUTLIER) cc_final: 0.2962 (t80) REVERT: B 146 HIS cc_start: 0.5080 (m90) cc_final: 0.4762 (m90) REVERT: B 176 PHE cc_start: 0.5931 (OUTLIER) cc_final: 0.5158 (m-80) outliers start: 46 outliers final: 25 residues processed: 93 average time/residue: 0.0760 time to fit residues: 10.1939 Evaluate side-chains 80 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 50 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 0.0770 chunk 76 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 559 HIS ** 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 = 0.4062 r_free = 0.4062 target = 0.138053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.105990 restraints weight = 19847.836| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.17 r_work: 0.3397 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9342 Z= 0.130 Angle : 0.708 11.853 12744 Z= 0.327 Chirality : 0.049 0.391 1462 Planarity : 0.004 0.065 1640 Dihedral : 12.761 107.913 1572 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 4.55 % Allowed : 21.95 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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 aren not related in a simple way. whole: -0.49 (0.25), residues: 1144 helix: -3.51 (1.34), residues: 12 sheet: 0.89 (0.23), residues: 498 loop : -1.33 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 480 TYR 0.010 0.001 TYR A 161 PHE 0.008 0.001 PHE B 135 TRP 0.010 0.001 TRP A 149 HIS 0.003 0.000 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9314) covalent geometry : angle 0.67516 (12672) SS BOND : bond 0.00175 ( 12) SS BOND : angle 0.77036 ( 24) hydrogen bonds : bond 0.02775 ( 318) hydrogen bonds : angle 5.11356 ( 750) link_ALPHA1-3 : bond 0.01834 ( 2) link_ALPHA1-3 : angle 2.05421 ( 6) link_BETA1-4 : bond 0.01083 ( 6) link_BETA1-4 : angle 3.69106 ( 18) link_NAG-ASN : bond 0.00824 ( 8) link_NAG-ASN : angle 3.67548 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 55 time to evaluate : 0.301 Fit side-chains REVERT: A 135 PHE cc_start: 0.4644 (OUTLIER) cc_final: 0.2745 (t80) REVERT: A 176 PHE cc_start: 0.6070 (OUTLIER) cc_final: 0.5374 (m-80) REVERT: A 544 TRP cc_start: 0.6061 (m100) cc_final: 0.5543 (m-10) REVERT: B 135 PHE cc_start: 0.4650 (OUTLIER) cc_final: 0.2755 (t80) outliers start: 44 outliers final: 25 residues processed: 92 average time/residue: 0.0659 time to fit residues: 9.5995 Evaluate side-chains 74 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 46 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.138024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.112239 restraints weight = 19676.306| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 4.79 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9342 Z= 0.149 Angle : 0.719 11.766 12744 Z= 0.333 Chirality : 0.049 0.401 1462 Planarity : 0.004 0.065 1640 Dihedral : 12.295 106.565 1572 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.77 % Favored : 94.06 % Rotamer: Outliers : 5.07 % Allowed : 22.05 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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 aren not related in a simple way. whole: -0.52 (0.25), residues: 1144 helix: -3.50 (1.34), residues: 12 sheet: 0.88 (0.24), residues: 498 loop : -1.36 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 480 TYR 0.010 0.001 TYR B 405 PHE 0.010 0.001 PHE A 245 TRP 0.008 0.002 TRP A 168 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9314) covalent geometry : angle 0.68595 (12672) SS BOND : bond 0.00205 ( 12) SS BOND : angle 1.05124 ( 24) hydrogen bonds : bond 0.02884 ( 318) hydrogen bonds : angle 5.11923 ( 750) link_ALPHA1-3 : bond 0.01745 ( 2) link_ALPHA1-3 : angle 2.15581 ( 6) link_BETA1-4 : bond 0.00992 ( 6) link_BETA1-4 : angle 3.73479 ( 18) link_NAG-ASN : bond 0.00741 ( 8) link_NAG-ASN : angle 3.64919 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 49 time to evaluate : 0.287 Fit side-chains REVERT: A 135 PHE cc_start: 0.4920 (OUTLIER) cc_final: 0.3158 (t80) REVERT: A 176 PHE cc_start: 0.5759 (OUTLIER) cc_final: 0.5078 (m-80) REVERT: A 387 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8307 (mm) REVERT: B 128 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.7074 (mtm180) REVERT: B 135 PHE cc_start: 0.5021 (OUTLIER) cc_final: 0.3266 (t80) REVERT: B 387 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8307 (mm) outliers start: 49 outliers final: 31 residues processed: 91 average time/residue: 0.0594 time to fit residues: 8.2176 Evaluate side-chains 82 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 45 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** B 559 HIS ** 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 = 0.4055 r_free = 0.4055 target = 0.137587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.111443 restraints weight = 19672.139| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 4.84 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9342 Z= 0.158 Angle : 0.724 11.568 12744 Z= 0.335 Chirality : 0.049 0.407 1462 Planarity : 0.005 0.068 1640 Dihedral : 12.029 105.229 1572 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.16 % Favored : 94.67 % Rotamer: Outliers : 4.87 % Allowed : 22.15 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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 aren not related in a simple way. whole: -0.52 (0.25), residues: 1144 helix: -3.54 (1.31), residues: 12 sheet: 0.86 (0.23), residues: 514 loop : -1.41 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 128 TYR 0.018 0.001 TYR A 161 PHE 0.010 0.001 PHE B 245 TRP 0.028 0.002 TRP A 544 HIS 0.004 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9314) covalent geometry : angle 0.69034 (12672) SS BOND : bond 0.00222 ( 12) SS BOND : angle 1.06465 ( 24) hydrogen bonds : bond 0.02922 ( 318) hydrogen bonds : angle 5.08781 ( 750) link_ALPHA1-3 : bond 0.01685 ( 2) link_ALPHA1-3 : angle 2.21198 ( 6) link_BETA1-4 : bond 0.00932 ( 6) link_BETA1-4 : angle 3.77511 ( 18) link_NAG-ASN : bond 0.00720 ( 8) link_NAG-ASN : angle 3.68426 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 44 time to evaluate : 0.327 Fit side-chains REVERT: A 135 PHE cc_start: 0.5029 (OUTLIER) cc_final: 0.3082 (t80) REVERT: A 176 PHE cc_start: 0.5794 (OUTLIER) cc_final: 0.5135 (m-80) REVERT: A 387 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8303 (mm) REVERT: B 128 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.7078 (mtm180) REVERT: B 135 PHE cc_start: 0.5120 (OUTLIER) cc_final: 0.3227 (t80) REVERT: B 164 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7103 (mt) REVERT: B 176 PHE cc_start: 0.5746 (OUTLIER) cc_final: 0.5005 (m-80) REVERT: B 229 LEU cc_start: 0.1254 (OUTLIER) cc_final: 0.0941 (pp) REVERT: B 387 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8303 (mm) outliers start: 47 outliers final: 30 residues processed: 83 average time/residue: 0.0682 time to fit residues: 8.7513 Evaluate side-chains 83 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 44 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 47 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** B 559 HIS ** 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 = 0.4061 r_free = 0.4061 target = 0.138095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.112977 restraints weight = 19572.541| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 4.51 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9342 Z= 0.133 Angle : 0.698 11.597 12744 Z= 0.321 Chirality : 0.048 0.394 1462 Planarity : 0.004 0.069 1640 Dihedral : 11.738 104.064 1572 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.81 % Favored : 95.02 % Rotamer: Outliers : 4.87 % Allowed : 22.05 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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 aren not related in a simple way. whole: -0.42 (0.25), residues: 1144 helix: -3.39 (1.41), residues: 12 sheet: 0.93 (0.23), residues: 514 loop : -1.34 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 480 TYR 0.009 0.001 TYR B 405 PHE 0.009 0.001 PHE A 245 TRP 0.011 0.001 TRP A 544 HIS 0.002 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9314) covalent geometry : angle 0.66396 (12672) SS BOND : bond 0.00192 ( 12) SS BOND : angle 0.92146 ( 24) hydrogen bonds : bond 0.02688 ( 318) hydrogen bonds : angle 4.93733 ( 750) link_ALPHA1-3 : bond 0.01651 ( 2) link_ALPHA1-3 : angle 2.24188 ( 6) link_BETA1-4 : bond 0.00969 ( 6) link_BETA1-4 : angle 3.68878 ( 18) link_NAG-ASN : bond 0.00781 ( 8) link_NAG-ASN : angle 3.67874 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 50 time to evaluate : 0.318 Fit side-chains REVERT: A 135 PHE cc_start: 0.5036 (OUTLIER) cc_final: 0.3113 (t80) REVERT: A 387 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8287 (mm) REVERT: B 135 PHE cc_start: 0.5021 (OUTLIER) cc_final: 0.3156 (t80) REVERT: B 176 PHE cc_start: 0.5630 (OUTLIER) cc_final: 0.4885 (m-80) REVERT: B 229 LEU cc_start: 0.1449 (OUTLIER) cc_final: 0.1085 (pp) REVERT: B 387 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8291 (mm) outliers start: 47 outliers final: 33 residues processed: 89 average time/residue: 0.0553 time to fit residues: 7.9614 Evaluate side-chains 84 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 45 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN 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 = 0.136394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.109961 restraints weight = 19459.685| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 4.74 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9342 Z= 0.203 Angle : 0.759 11.535 12744 Z= 0.355 Chirality : 0.051 0.428 1462 Planarity : 0.005 0.070 1640 Dihedral : 11.777 103.721 1572 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.12 % Favored : 93.62 % Rotamer: Outliers : 5.28 % Allowed : 21.74 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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 aren not related in a simple way. whole: -0.66 (0.25), residues: 1144 helix: -3.56 (1.30), residues: 12 sheet: 0.81 (0.23), residues: 502 loop : -1.51 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 443 TYR 0.011 0.001 TYR A 405 PHE 0.012 0.002 PHE B 245 TRP 0.013 0.002 TRP A 544 HIS 0.005 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 9314) covalent geometry : angle 0.72649 (12672) SS BOND : bond 0.00251 ( 12) SS BOND : angle 1.16956 ( 24) hydrogen bonds : bond 0.03293 ( 318) hydrogen bonds : angle 5.25334 ( 750) link_ALPHA1-3 : bond 0.01562 ( 2) link_ALPHA1-3 : angle 2.35896 ( 6) link_BETA1-4 : bond 0.00779 ( 6) link_BETA1-4 : angle 3.73119 ( 18) link_NAG-ASN : bond 0.00635 ( 8) link_NAG-ASN : angle 3.75338 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 43 time to evaluate : 0.213 Fit side-chains REVERT: A 135 PHE cc_start: 0.5348 (OUTLIER) cc_final: 0.3321 (t80) REVERT: A 176 PHE cc_start: 0.5866 (OUTLIER) cc_final: 0.5185 (m-80) REVERT: A 387 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8348 (mm) REVERT: B 135 PHE cc_start: 0.5326 (OUTLIER) cc_final: 0.3362 (t80) REVERT: B 176 PHE cc_start: 0.5701 (OUTLIER) cc_final: 0.5003 (m-80) REVERT: B 229 LEU cc_start: 0.1953 (OUTLIER) cc_final: 0.1525 (pp) REVERT: B 387 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8307 (mm) outliers start: 51 outliers final: 38 residues processed: 87 average time/residue: 0.0535 time to fit residues: 7.6880 Evaluate side-chains 87 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 42 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** B 559 HIS ** 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 = 0.4030 r_free = 0.4030 target = 0.135739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.108921 restraints weight = 19570.563| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 4.96 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9342 Z= 0.211 Angle : 0.769 11.623 12744 Z= 0.361 Chirality : 0.051 0.438 1462 Planarity : 0.005 0.070 1640 Dihedral : 11.737 102.924 1572 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.03 % Favored : 93.79 % Rotamer: Outliers : 5.07 % Allowed : 22.36 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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 aren not related in a simple way. whole: -0.81 (0.25), residues: 1144 helix: -3.57 (1.29), residues: 12 sheet: 0.66 (0.23), residues: 522 loop : -1.64 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 480 TYR 0.011 0.002 TYR B 405 PHE 0.012 0.002 PHE A 245 TRP 0.012 0.002 TRP A 544 HIS 0.002 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 9314) covalent geometry : angle 0.73468 (12672) SS BOND : bond 0.00236 ( 12) SS BOND : angle 1.19262 ( 24) hydrogen bonds : bond 0.03346 ( 318) hydrogen bonds : angle 5.32622 ( 750) link_ALPHA1-3 : bond 0.01524 ( 2) link_ALPHA1-3 : angle 2.38667 ( 6) link_BETA1-4 : bond 0.00768 ( 6) link_BETA1-4 : angle 3.77969 ( 18) link_NAG-ASN : bond 0.00671 ( 8) link_NAG-ASN : angle 3.90088 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 45 time to evaluate : 0.261 Fit side-chains REVERT: A 135 PHE cc_start: 0.5432 (OUTLIER) cc_final: 0.3337 (t80) REVERT: A 176 PHE cc_start: 0.6069 (OUTLIER) cc_final: 0.5443 (m-80) REVERT: A 387 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8303 (mm) REVERT: B 135 PHE cc_start: 0.5399 (OUTLIER) cc_final: 0.3443 (t80) REVERT: B 173 PHE cc_start: 0.5231 (OUTLIER) cc_final: 0.4670 (m-80) REVERT: B 176 PHE cc_start: 0.5645 (OUTLIER) cc_final: 0.5005 (m-80) REVERT: B 387 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8314 (mm) outliers start: 49 outliers final: 36 residues processed: 86 average time/residue: 0.0565 time to fit residues: 7.8291 Evaluate side-chains 85 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 42 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 23 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** B 559 HIS ** 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 = 0.4054 r_free = 0.4054 target = 0.137488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.110580 restraints weight = 19485.407| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 5.03 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9342 Z= 0.135 Angle : 0.717 11.572 12744 Z= 0.331 Chirality : 0.049 0.398 1462 Planarity : 0.004 0.071 1640 Dihedral : 11.460 101.932 1572 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.81 % Favored : 95.02 % Rotamer: Outliers : 4.97 % Allowed : 22.57 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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 aren not related in a simple way. whole: -0.63 (0.25), residues: 1144 helix: -3.43 (1.38), residues: 12 sheet: 0.74 (0.23), residues: 524 loop : -1.48 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 480 TYR 0.009 0.001 TYR B 405 PHE 0.008 0.001 PHE A 245 TRP 0.011 0.002 TRP A 544 HIS 0.002 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9314) covalent geometry : angle 0.68280 (12672) SS BOND : bond 0.00204 ( 12) SS BOND : angle 0.99772 ( 24) hydrogen bonds : bond 0.02743 ( 318) hydrogen bonds : angle 5.00046 ( 750) link_ALPHA1-3 : bond 0.01599 ( 2) link_ALPHA1-3 : angle 2.38339 ( 6) link_BETA1-4 : bond 0.00905 ( 6) link_BETA1-4 : angle 3.64530 ( 18) link_NAG-ASN : bond 0.00796 ( 8) link_NAG-ASN : angle 3.82115 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 46 time to evaluate : 0.270 Fit side-chains REVERT: A 135 PHE cc_start: 0.5323 (OUTLIER) cc_final: 0.3243 (t80) REVERT: A 176 PHE cc_start: 0.5830 (OUTLIER) cc_final: 0.5195 (m-80) REVERT: A 387 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8259 (mm) REVERT: B 135 PHE cc_start: 0.5269 (OUTLIER) cc_final: 0.3224 (t80) REVERT: B 173 PHE cc_start: 0.5116 (OUTLIER) cc_final: 0.4584 (m-80) REVERT: B 176 PHE cc_start: 0.5596 (OUTLIER) cc_final: 0.4887 (m-80) REVERT: B 387 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8273 (mm) outliers start: 48 outliers final: 38 residues processed: 87 average time/residue: 0.0529 time to fit residues: 7.2184 Evaluate side-chains 90 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 45 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 549 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 0.3980 chunk 97 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.138997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.112144 restraints weight = 19322.700| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 4.95 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9342 Z= 0.115 Angle : 0.698 11.683 12744 Z= 0.319 Chirality : 0.048 0.365 1462 Planarity : 0.004 0.071 1640 Dihedral : 11.092 100.466 1572 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.72 % Favored : 95.10 % Rotamer: Outliers : 3.93 % Allowed : 23.71 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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 aren not related in a simple way. whole: -0.35 (0.26), residues: 1144 helix: -3.20 (1.53), residues: 12 sheet: 0.97 (0.23), residues: 514 loop : -1.30 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 140 TYR 0.009 0.001 TYR A 161 PHE 0.008 0.001 PHE B 382 TRP 0.014 0.001 TRP A 149 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9314) covalent geometry : angle 0.66533 (12672) SS BOND : bond 0.00177 ( 12) SS BOND : angle 0.86354 ( 24) hydrogen bonds : bond 0.02458 ( 318) hydrogen bonds : angle 4.74982 ( 750) link_ALPHA1-3 : bond 0.01565 ( 2) link_ALPHA1-3 : angle 2.40439 ( 6) link_BETA1-4 : bond 0.00947 ( 6) link_BETA1-4 : angle 3.49841 ( 18) link_NAG-ASN : bond 0.00852 ( 8) link_NAG-ASN : angle 3.68883 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1907.88 seconds wall clock time: 33 minutes 19.76 seconds (1999.76 seconds total)