Starting phenix.real_space_refine on Mon May 12 18:44:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3j_36853/05_2025/8k3j_36853.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3j_36853/05_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_36853/05_2025/8k3j_36853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3j_36853/05_2025/8k3j_36853.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3j_36853/05_2025/8k3j_36853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3j_36853/05_2025/8k3j_36853.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.78, per 1000 atoms: 0.74 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: 2.63 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.62 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: 3.57 Time building geometry restraints manager: 3.04 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: 0.05 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: 3.920 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.650 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.001 TRP A 149 HIS 0.003 0.001 HIS A 559 PHE 0.008 0.001 PHE B 135 TYR 0.007 0.001 TYR B 405 ARG 0.002 0.000 ARG B 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00947 ( 8) link_NAG-ASN : angle 4.47192 ( 24) link_BETA1-4 : bond 0.00851 ( 6) link_BETA1-4 : angle 3.29041 ( 18) link_ALPHA1-3 : bond 0.00846 ( 2) link_ALPHA1-3 : angle 1.52032 ( 6) hydrogen bonds : bond 0.14758 ( 318) hydrogen bonds : angle 6.16753 ( 750) SS BOND : bond 0.00191 ( 12) SS BOND : angle 0.76769 ( 24) covalent geometry : bond 0.00418 ( 9314) covalent geometry : angle 0.68726 (12672) *********************** 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 : 0.909 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 0.1698 time to fit residues: 14.3871 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 : 0.920 ------------------------------------------------------------------------------- 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 96 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.138956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.104066 restraints weight = 19453.944| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.13 r_work: 0.3426 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.0578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9342 Z= 0.139 Angle : 0.698 11.362 12744 Z= 0.327 Chirality : 0.050 0.384 1462 Planarity : 0.004 0.049 1640 Dihedral : 15.969 109.507 1575 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.33 % Favored : 94.49 % Rotamer: Outliers : 3.31 % Allowed : 22.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.25), residues: 1144 helix: -3.19 (1.54), residues: 12 sheet: 0.72 (0.23), residues: 524 loop : -1.31 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 149 HIS 0.003 0.001 HIS B 146 PHE 0.009 0.001 PHE B 245 TYR 0.009 0.001 TYR B 405 ARG 0.004 0.000 ARG A 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00821 ( 8) link_NAG-ASN : angle 3.47005 ( 24) link_BETA1-4 : bond 0.01083 ( 6) link_BETA1-4 : angle 3.20036 ( 18) link_ALPHA1-3 : bond 0.02133 ( 2) link_ALPHA1-3 : angle 1.40611 ( 6) hydrogen bonds : bond 0.03409 ( 318) hydrogen bonds : angle 5.35423 ( 750) SS BOND : bond 0.00199 ( 12) SS BOND : angle 0.70372 ( 24) covalent geometry : bond 0.00320 ( 9314) covalent geometry : angle 0.67116 (12672) *********************** 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 85 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 53 time to evaluate : 0.942 Fit side-chains REVERT: A 544 TRP cc_start: 0.5714 (m100) cc_final: 0.4905 (m-10) outliers start: 32 outliers final: 17 residues processed: 82 average time/residue: 0.1764 time to fit residues: 21.9239 Evaluate side-chains 66 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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 164 LEU Chi-restraints excluded: chain B residue 169 LEU 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 42 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN B 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.138379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.112902 restraints weight = 19675.260| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 4.75 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9342 Z= 0.147 Angle : 0.714 12.042 12744 Z= 0.331 Chirality : 0.050 0.394 1462 Planarity : 0.004 0.061 1640 Dihedral : 13.408 109.288 1572 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.45 % Allowed : 21.22 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.25), residues: 1144 helix: -3.62 (1.26), residues: 12 sheet: 0.89 (0.23), residues: 498 loop : -1.28 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 149 HIS 0.004 0.001 HIS A 146 PHE 0.011 0.001 PHE A 245 TYR 0.018 0.001 TYR A 161 ARG 0.003 0.000 ARG B 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00713 ( 8) link_NAG-ASN : angle 3.58033 ( 24) link_BETA1-4 : bond 0.01089 ( 6) link_BETA1-4 : angle 3.51668 ( 18) link_ALPHA1-3 : bond 0.01922 ( 2) link_ALPHA1-3 : angle 1.95843 ( 6) hydrogen bonds : bond 0.02995 ( 318) hydrogen bonds : angle 5.14045 ( 750) SS BOND : bond 0.00201 ( 12) SS BOND : angle 0.74563 ( 24) covalent geometry : bond 0.00349 ( 9314) covalent geometry : angle 0.68425 (12672) *********************** 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 99 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 56 time to evaluate : 1.022 Fit side-chains REVERT: A 176 PHE cc_start: 0.5721 (OUTLIER) cc_final: 0.5120 (m-80) REVERT: A 544 TRP cc_start: 0.5859 (m100) cc_final: 0.5619 (m-10) REVERT: B 128 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6932 (mtm180) REVERT: B 135 PHE cc_start: 0.4414 (OUTLIER) cc_final: 0.2873 (t80) outliers start: 43 outliers final: 23 residues processed: 94 average time/residue: 0.1864 time to fit residues: 25.9659 Evaluate side-chains 77 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 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 403 THR 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 119 THR 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 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 465 VAL Chi-restraints excluded: chain B residue 473 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 76 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 79 optimal weight: 0.0000 chunk 48 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- 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** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.135020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.099156 restraints weight = 19547.655| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.27 r_work: 0.3303 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 9342 Z= 0.309 Angle : 0.858 11.220 12744 Z= 0.410 Chirality : 0.055 0.475 1462 Planarity : 0.006 0.067 1640 Dihedral : 12.889 108.659 1572 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.69 % Favored : 92.05 % Rotamer: Outliers : 5.80 % Allowed : 21.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.25), residues: 1144 helix: -4.03 (0.98), residues: 12 sheet: 0.70 (0.23), residues: 502 loop : -1.66 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 149 HIS 0.003 0.001 HIS B 534 PHE 0.014 0.002 PHE A 245 TYR 0.013 0.002 TYR A 405 ARG 0.004 0.001 ARG A 443 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 8) link_NAG-ASN : angle 3.92654 ( 24) link_BETA1-4 : bond 0.00718 ( 6) link_BETA1-4 : angle 3.94703 ( 18) link_ALPHA1-3 : bond 0.01805 ( 2) link_ALPHA1-3 : angle 2.24475 ( 6) hydrogen bonds : bond 0.04136 ( 318) hydrogen bonds : angle 5.81279 ( 750) SS BOND : bond 0.00382 ( 12) SS BOND : angle 1.42142 ( 24) covalent geometry : bond 0.00764 ( 9314) covalent geometry : angle 0.82673 (12672) *********************** 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 106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 50 time to evaluate : 0.940 Fit side-chains REVERT: A 135 PHE cc_start: 0.5358 (OUTLIER) cc_final: 0.3255 (t80) REVERT: A 176 PHE cc_start: 0.6169 (OUTLIER) cc_final: 0.5497 (m-80) REVERT: A 387 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8521 (mm) REVERT: B 128 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7667 (mtm-85) REVERT: B 135 PHE cc_start: 0.5435 (OUTLIER) cc_final: 0.3298 (t80) REVERT: B 176 PHE cc_start: 0.5929 (OUTLIER) cc_final: 0.5244 (m-80) REVERT: B 387 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8523 (mm) outliers start: 56 outliers final: 33 residues processed: 100 average time/residue: 0.1493 time to fit residues: 23.3474 Evaluate side-chains 84 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 44 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 222 SER 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 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 576 ASN 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 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 212 HIS Chi-restraints excluded: chain B residue 222 SER 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 450 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 0.0770 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.136696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.110904 restraints weight = 19457.364| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 4.85 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1602 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= 0.151 Angle : 0.735 11.446 12744 Z= 0.342 Chirality : 0.050 0.418 1462 Planarity : 0.005 0.069 1640 Dihedral : 12.391 106.084 1572 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.24 % Favored : 94.58 % Rotamer: Outliers : 4.04 % Allowed : 23.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.25), residues: 1144 helix: -3.58 (1.30), residues: 12 sheet: 0.74 (0.23), residues: 522 loop : -1.55 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 168 HIS 0.003 0.001 HIS B 559 PHE 0.009 0.001 PHE B 245 TYR 0.010 0.001 TYR A 161 ARG 0.003 0.000 ARG A 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00773 ( 8) link_NAG-ASN : angle 3.87634 ( 24) link_BETA1-4 : bond 0.00974 ( 6) link_BETA1-4 : angle 3.84904 ( 18) link_ALPHA1-3 : bond 0.01738 ( 2) link_ALPHA1-3 : angle 2.15353 ( 6) hydrogen bonds : bond 0.02953 ( 318) hydrogen bonds : angle 5.30271 ( 750) SS BOND : bond 0.00213 ( 12) SS BOND : angle 1.11961 ( 24) covalent geometry : bond 0.00357 ( 9314) covalent geometry : angle 0.69898 (12672) *********************** 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 83 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 44 time to evaluate : 0.984 Fit side-chains REVERT: A 135 PHE cc_start: 0.5045 (OUTLIER) cc_final: 0.3069 (t80) REVERT: A 176 PHE cc_start: 0.5912 (OUTLIER) cc_final: 0.5176 (m-80) REVERT: B 128 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.7096 (mtm180) REVERT: B 135 PHE cc_start: 0.5055 (OUTLIER) cc_final: 0.3200 (t80) REVERT: B 176 PHE cc_start: 0.5655 (OUTLIER) cc_final: 0.4921 (m-80) outliers start: 39 outliers final: 26 residues processed: 76 average time/residue: 0.1592 time to fit residues: 19.0869 Evaluate side-chains 74 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 43 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 166 TYR 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 465 VAL Chi-restraints excluded: chain A residue 576 ASN 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 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 310 ASN Chi-restraints excluded: chain B residue 438 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 0.0270 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.137766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.103651 restraints weight = 19570.709| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.29 r_work: 0.3378 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9342 Z= 0.125 Angle : 0.698 11.609 12744 Z= 0.321 Chirality : 0.048 0.389 1462 Planarity : 0.004 0.069 1640 Dihedral : 11.816 104.353 1572 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.24 % Favored : 94.58 % Rotamer: Outliers : 5.38 % Allowed : 22.46 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.25), residues: 1144 helix: -3.39 (1.41), residues: 12 sheet: 1.04 (0.23), residues: 490 loop : -1.40 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.003 0.001 HIS A 559 PHE 0.008 0.001 PHE B 245 TYR 0.008 0.001 TYR B 405 ARG 0.003 0.000 ARG B 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00828 ( 8) link_NAG-ASN : angle 3.69147 ( 24) link_BETA1-4 : bond 0.00998 ( 6) link_BETA1-4 : angle 3.73250 ( 18) link_ALPHA1-3 : bond 0.01690 ( 2) link_ALPHA1-3 : angle 2.19588 ( 6) hydrogen bonds : bond 0.02596 ( 318) hydrogen bonds : angle 4.90492 ( 750) SS BOND : bond 0.00176 ( 12) SS BOND : angle 0.87211 ( 24) covalent geometry : bond 0.00290 ( 9314) covalent geometry : angle 0.66399 (12672) *********************** 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 103 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 51 time to evaluate : 0.943 Fit side-chains REVERT: A 135 PHE cc_start: 0.5154 (OUTLIER) cc_final: 0.2957 (t80) REVERT: A 176 PHE cc_start: 0.5966 (OUTLIER) cc_final: 0.5243 (m-80) REVERT: A 387 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8459 (mm) REVERT: B 128 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7644 (mtm180) REVERT: B 135 PHE cc_start: 0.5169 (OUTLIER) cc_final: 0.2979 (t80) REVERT: B 164 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7240 (mt) REVERT: B 176 PHE cc_start: 0.5824 (OUTLIER) cc_final: 0.5027 (m-80) REVERT: B 229 LEU cc_start: 0.2058 (OUTLIER) cc_final: 0.1656 (pp) REVERT: B 387 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8468 (mm) outliers start: 52 outliers final: 38 residues processed: 94 average time/residue: 0.1500 time to fit residues: 22.2583 Evaluate side-chains 92 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 45 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 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 204 ASN Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 222 SER 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 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 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 222 SER 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 387 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 38 optimal weight: 0.0470 chunk 5 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.1284 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.136865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.110814 restraints weight = 19663.233| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 5.16 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1804 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= 0.159 Angle : 0.718 11.461 12744 Z= 0.333 Chirality : 0.049 0.401 1462 Planarity : 0.005 0.069 1640 Dihedral : 11.731 103.877 1572 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.42 % Favored : 94.41 % Rotamer: Outliers : 6.63 % Allowed : 21.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1144 helix: -3.44 (1.38), residues: 12 sheet: 0.87 (0.23), residues: 514 loop : -1.41 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 544 HIS 0.002 0.001 HIS A 146 PHE 0.011 0.001 PHE A 245 TYR 0.010 0.001 TYR B 405 ARG 0.002 0.000 ARG B 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 8) link_NAG-ASN : angle 3.69601 ( 24) link_BETA1-4 : bond 0.00899 ( 6) link_BETA1-4 : angle 3.68466 ( 18) link_ALPHA1-3 : bond 0.01624 ( 2) link_ALPHA1-3 : angle 2.27764 ( 6) hydrogen bonds : bond 0.02906 ( 318) hydrogen bonds : angle 5.04850 ( 750) SS BOND : bond 0.00191 ( 12) SS BOND : angle 0.96246 ( 24) covalent geometry : bond 0.00384 ( 9314) covalent geometry : angle 0.68542 (12672) *********************** 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 108 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 44 time to evaluate : 1.058 Fit side-chains REVERT: A 135 PHE cc_start: 0.5183 (OUTLIER) cc_final: 0.3182 (t80) REVERT: A 176 PHE cc_start: 0.5827 (OUTLIER) cc_final: 0.5113 (m-80) REVERT: A 387 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8289 (mm) REVERT: A 436 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8401 (tp) REVERT: B 128 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7177 (mtm180) REVERT: B 135 PHE cc_start: 0.5207 (OUTLIER) cc_final: 0.3187 (t80) REVERT: B 173 PHE cc_start: 0.5105 (OUTLIER) cc_final: 0.4628 (m-80) REVERT: B 176 PHE cc_start: 0.5676 (OUTLIER) cc_final: 0.4946 (m-80) REVERT: B 229 LEU cc_start: 0.1965 (OUTLIER) cc_final: 0.1572 (pp) REVERT: B 387 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8306 (mm) outliers start: 64 outliers final: 44 residues processed: 100 average time/residue: 0.1497 time to fit residues: 23.7058 Evaluate side-chains 96 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 42 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 90 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 222 SER 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 436 ILE Chi-restraints excluded: chain A residue 438 ILE 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 45 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 112 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 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 222 SER 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 450 VAL 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 Chi-restraints excluded: chain B residue 576 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 61 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.0570 chunk 97 optimal weight: 4.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.137933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.102923 restraints weight = 19916.241| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.18 r_work: 0.3399 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9342 Z= 0.122 Angle : 0.692 11.597 12744 Z= 0.317 Chirality : 0.048 0.379 1462 Planarity : 0.004 0.070 1640 Dihedral : 11.498 102.901 1572 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.63 % Favored : 95.19 % Rotamer: Outliers : 5.18 % Allowed : 22.67 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.26), residues: 1144 helix: -3.33 (1.45), residues: 12 sheet: 0.95 (0.23), residues: 514 loop : -1.31 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 544 HIS 0.003 0.001 HIS B 559 PHE 0.008 0.001 PHE A 245 TYR 0.009 0.001 TYR B 405 ARG 0.002 0.000 ARG B 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00810 ( 8) link_NAG-ASN : angle 3.69140 ( 24) link_BETA1-4 : bond 0.00981 ( 6) link_BETA1-4 : angle 3.59647 ( 18) link_ALPHA1-3 : bond 0.01626 ( 2) link_ALPHA1-3 : angle 2.28065 ( 6) hydrogen bonds : bond 0.02559 ( 318) hydrogen bonds : angle 4.84046 ( 750) SS BOND : bond 0.00173 ( 12) SS BOND : angle 0.85592 ( 24) covalent geometry : bond 0.00283 ( 9314) covalent geometry : angle 0.65802 (12672) *********************** 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 95 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 45 time to evaluate : 0.962 Fit side-chains REVERT: A 135 PHE cc_start: 0.5408 (OUTLIER) cc_final: 0.3196 (t80) REVERT: A 176 PHE cc_start: 0.5928 (OUTLIER) cc_final: 0.5231 (m-80) REVERT: B 128 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7604 (mtm180) REVERT: B 134 GLU cc_start: 0.7112 (tp30) cc_final: 0.6878 (mm-30) REVERT: B 135 PHE cc_start: 0.5423 (OUTLIER) cc_final: 0.3350 (t80) REVERT: B 173 PHE cc_start: 0.4900 (OUTLIER) cc_final: 0.4350 (m-80) REVERT: B 176 PHE cc_start: 0.5798 (OUTLIER) cc_final: 0.5048 (m-80) REVERT: B 229 LEU cc_start: 0.2397 (OUTLIER) cc_final: 0.2053 (pp) outliers start: 50 outliers final: 40 residues processed: 88 average time/residue: 0.1579 time to fit residues: 21.9597 Evaluate side-chains 90 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 43 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 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 222 SER 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 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 34 THR 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 112 LEU 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 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 222 SER 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 403 THR Chi-restraints excluded: chain B residue 438 ILE 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 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 39 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.137560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.102553 restraints weight = 19380.173| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.82 r_work: 0.3418 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9342 Z= 0.138 Angle : 0.703 11.571 12744 Z= 0.323 Chirality : 0.048 0.385 1462 Planarity : 0.004 0.067 1640 Dihedral : 11.370 102.243 1572 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.81 % Favored : 95.02 % Rotamer: Outliers : 5.49 % Allowed : 22.77 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.26), residues: 1144 helix: -3.31 (1.46), residues: 12 sheet: 0.94 (0.23), residues: 514 loop : -1.33 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 149 HIS 0.002 0.001 HIS A 146 PHE 0.010 0.001 PHE A 245 TYR 0.009 0.001 TYR B 405 ARG 0.002 0.000 ARG B 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00742 ( 8) link_NAG-ASN : angle 3.65495 ( 24) link_BETA1-4 : bond 0.00899 ( 6) link_BETA1-4 : angle 3.55907 ( 18) link_ALPHA1-3 : bond 0.01581 ( 2) link_ALPHA1-3 : angle 2.35617 ( 6) hydrogen bonds : bond 0.02693 ( 318) hydrogen bonds : angle 4.88756 ( 750) SS BOND : bond 0.00182 ( 12) SS BOND : angle 0.87465 ( 24) covalent geometry : bond 0.00329 ( 9314) covalent geometry : angle 0.67034 (12672) *********************** 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 96 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 43 time to evaluate : 0.996 Fit side-chains REVERT: A 135 PHE cc_start: 0.5348 (OUTLIER) cc_final: 0.3102 (t80) REVERT: A 176 PHE cc_start: 0.5949 (OUTLIER) cc_final: 0.5306 (m-80) REVERT: B 128 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7550 (mtm180) REVERT: B 135 PHE cc_start: 0.5299 (OUTLIER) cc_final: 0.3086 (t80) REVERT: B 173 PHE cc_start: 0.4864 (OUTLIER) cc_final: 0.4303 (m-80) REVERT: B 176 PHE cc_start: 0.5812 (OUTLIER) cc_final: 0.5067 (m-80) REVERT: B 229 LEU cc_start: 0.2420 (OUTLIER) cc_final: 0.2123 (pp) REVERT: B 387 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8458 (mm) outliers start: 53 outliers final: 42 residues processed: 89 average time/residue: 0.1585 time to fit residues: 21.9416 Evaluate side-chains 93 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 43 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 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 222 SER 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 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 34 THR 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 112 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 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 222 SER 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 450 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 62 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 0.0040 chunk 79 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.138594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.112599 restraints weight = 19910.116| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 4.91 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9342 Z= 0.110 Angle : 0.683 11.767 12744 Z= 0.310 Chirality : 0.047 0.359 1462 Planarity : 0.004 0.067 1640 Dihedral : 11.113 100.932 1572 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.37 % Favored : 95.45 % Rotamer: Outliers : 5.49 % Allowed : 22.77 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1144 helix: -3.33 (1.44), residues: 12 sheet: 1.15 (0.24), residues: 490 loop : -1.26 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 544 HIS 0.002 0.000 HIS A 88 PHE 0.009 0.001 PHE B 382 TYR 0.008 0.001 TYR B 405 ARG 0.002 0.000 ARG B 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00832 ( 8) link_NAG-ASN : angle 3.61764 ( 24) link_BETA1-4 : bond 0.00953 ( 6) link_BETA1-4 : angle 3.46631 ( 18) link_ALPHA1-3 : bond 0.01581 ( 2) link_ALPHA1-3 : angle 2.37355 ( 6) hydrogen bonds : bond 0.02421 ( 318) hydrogen bonds : angle 4.69076 ( 750) SS BOND : bond 0.00176 ( 12) SS BOND : angle 0.81148 ( 24) covalent geometry : bond 0.00251 ( 9314) covalent geometry : angle 0.65063 (12672) ********************** 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 104 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 51 time to evaluate : 1.017 Fit side-chains REVERT: A 134 GLU cc_start: 0.6797 (tp30) cc_final: 0.6526 (mm-30) REVERT: A 135 PHE cc_start: 0.5177 (OUTLIER) cc_final: 0.3283 (t80) REVERT: A 173 PHE cc_start: 0.4971 (OUTLIER) cc_final: 0.4619 (m-80) REVERT: A 176 PHE cc_start: 0.5711 (OUTLIER) cc_final: 0.5019 (m-80) REVERT: A 436 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8400 (tp) REVERT: B 128 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.7104 (mtm180) REVERT: B 135 PHE cc_start: 0.5191 (OUTLIER) cc_final: 0.3302 (t80) REVERT: B 173 PHE cc_start: 0.5037 (OUTLIER) cc_final: 0.4590 (m-80) REVERT: B 176 PHE cc_start: 0.5671 (OUTLIER) cc_final: 0.4920 (m-80) outliers start: 53 outliers final: 41 residues processed: 96 average time/residue: 0.1604 time to fit residues: 23.8963 Evaluate side-chains 93 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 44 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 119 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 173 PHE 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 222 SER 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 403 THR Chi-restraints excluded: chain A residue 436 ILE 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 563 THR 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 112 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 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 222 SER 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 403 THR Chi-restraints excluded: chain B residue 438 ILE 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 509 THR Chi-restraints excluded: chain B residue 540 LEU 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 70 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 98 optimal weight: 0.0050 chunk 55 optimal weight: 7.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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** ** 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 = 0.4074 r_free = 0.4074 target = 0.138776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.104273 restraints weight = 19680.367| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.19 r_work: 0.3401 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9342 Z= 0.114 Angle : 0.690 11.783 12744 Z= 0.314 Chirality : 0.047 0.358 1462 Planarity : 0.004 0.067 1640 Dihedral : 10.957 100.158 1572 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.28 % Favored : 95.54 % Rotamer: Outliers : 5.38 % Allowed : 22.77 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1144 helix: -3.34 (1.43), residues: 12 sheet: 1.14 (0.24), residues: 492 loop : -1.23 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 544 HIS 0.001 0.000 HIS A 146 PHE 0.008 0.001 PHE A 245 TYR 0.008 0.001 TYR A 405 ARG 0.002 0.000 ARG B 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00800 ( 8) link_NAG-ASN : angle 3.57324 ( 24) link_BETA1-4 : bond 0.00919 ( 6) link_BETA1-4 : angle 3.42999 ( 18) link_ALPHA1-3 : bond 0.01557 ( 2) link_ALPHA1-3 : angle 2.43282 ( 6) hydrogen bonds : bond 0.02419 ( 318) hydrogen bonds : angle 4.68278 ( 750) SS BOND : bond 0.00167 ( 12) SS BOND : angle 0.78007 ( 24) covalent geometry : bond 0.00265 ( 9314) covalent geometry : angle 0.65897 (12672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4945.09 seconds wall clock time: 86 minutes 30.45 seconds (5190.45 seconds total)