Starting phenix.real_space_refine on Tue May 13 16:15:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xv1_38689/05_2025/8xv1_38689.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xv1_38689/05_2025/8xv1_38689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xv1_38689/05_2025/8xv1_38689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xv1_38689/05_2025/8xv1_38689.map" model { file = "/net/cci-nas-00/data/ceres_data/8xv1_38689/05_2025/8xv1_38689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xv1_38689/05_2025/8xv1_38689.cif" } resolution = 3.05 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4890 atoms to isotropic. 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 37 5.16 5 C 4254 2.51 5 N 1084 2.21 5 O 1277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6652 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1592 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 13, 'TRANS': 184} Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "L" 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.80, per 1000 atoms: 0.72 Number of scatterers: 6652 At special positions: 0 Unit cell: (102.51, 96.48, 111.555, 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 37 16.00 O 1277 8.00 N 1084 7.00 C 4254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 487 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " 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 N 3 " - " MAN N 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 354 " " NAG D 701 " - " ASN D 322 " " NAG D 702 " - " ASN D 432 " " NAG D 703 " - " ASN D 53 " " NAG L 1 " - " ASN D 546 " " NAG M 1 " - " ASN D 90 " " NAG N 1 " - " ASN D 103 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 867.8 milliseconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1498 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 6 sheets defined 53.4% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.555A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.664A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 81 Processing helix chain 'D' and resid 92 through 104 removed outlier: 3.697A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 144 through 155 removed outlier: 4.276A pdb=" N ASN D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 195 removed outlier: 3.996A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 4.035A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 4.020A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.701A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.934A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.831A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 412 removed outlier: 3.998A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.744A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.787A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.686A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.558A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.732A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A 396 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.696A pdb=" N TYR A 488 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.059A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 350 302 hydrogen bonds defined for protein. 867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2090 1.34 - 1.46: 1700 1.46 - 1.58: 2993 1.58 - 1.70: 0 1.70 - 1.81: 58 Bond restraints: 6841 Sorted by residual: bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" C1 NAG D 702 " pdb=" O5 NAG D 702 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.12e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.00e+00 ... (remaining 6836 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 8945 1.26 - 2.52: 257 2.52 - 3.78: 63 3.78 - 5.04: 22 5.04 - 6.30: 10 Bond angle restraints: 9297 Sorted by residual: angle pdb=" CA GLY A 416 " pdb=" C GLY A 416 " pdb=" N ASN A 417 " ideal model delta sigma weight residual 114.23 117.04 -2.81 8.80e-01 1.29e+00 1.02e+01 angle pdb=" CA GLY A 416 " pdb=" C GLY A 416 " pdb=" O GLY A 416 " ideal model delta sigma weight residual 122.33 120.21 2.12 8.10e-01 1.52e+00 6.86e+00 angle pdb=" NE ARG A 466 " pdb=" CZ ARG A 466 " pdb=" NH2 ARG A 466 " ideal model delta sigma weight residual 119.20 121.50 -2.30 9.00e-01 1.23e+00 6.50e+00 angle pdb=" N LYS D 234 " pdb=" CA LYS D 234 " pdb=" C LYS D 234 " ideal model delta sigma weight residual 113.77 116.99 -3.22 1.32e+00 5.74e-01 5.95e+00 angle pdb=" N LEU A 517 " pdb=" CA LEU A 517 " pdb=" C LEU A 517 " ideal model delta sigma weight residual 108.45 111.45 -3.00 1.26e+00 6.30e-01 5.68e+00 ... (remaining 9292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 3886 21.82 - 43.63: 281 43.63 - 65.45: 34 65.45 - 87.27: 19 87.27 - 109.09: 8 Dihedral angle restraints: 4228 sinusoidal: 1895 harmonic: 2333 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 487 " pdb=" CB CYS A 487 " ideal model delta sinusoidal sigma weight residual 93.00 165.83 -72.83 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CB CYS D 530 " pdb=" SG CYS D 530 " pdb=" SG CYS D 542 " pdb=" CB CYS D 542 " ideal model delta sinusoidal sigma weight residual -86.00 -133.68 47.68 1 1.00e+01 1.00e-02 3.14e+01 dihedral pdb=" SG CYS A 391 " pdb=" CB CYS A 524 " pdb=" SG CYS A 524 " pdb=" CA CYS A 524 " ideal model delta sinusoidal sigma weight residual 79.00 10.69 68.31 1 2.00e+01 2.50e-03 1.51e+01 ... (remaining 4225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1000 0.118 - 0.236: 8 0.236 - 0.354: 4 0.354 - 0.472: 0 0.472 - 0.590: 1 Chirality restraints: 1013 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.71e+00 chirality pdb=" C1 NAG D 701 " pdb=" ND2 ASN D 322 " pdb=" C2 NAG D 701 " pdb=" O5 NAG D 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 1010 not shown) Planarity restraints: 1188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 519 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO A 520 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 520 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 520 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 103 " 0.014 2.00e-02 2.50e+03 1.34e-02 2.24e+00 pdb=" CG ASN D 103 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN D 103 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN D 103 " -0.019 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.15e+00 pdb=" N PRO A 337 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " -0.015 5.00e-02 4.00e+02 ... (remaining 1185 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1305 2.78 - 3.31: 6166 3.31 - 3.84: 10592 3.84 - 4.37: 11790 4.37 - 4.90: 21126 Nonbonded interactions: 50979 Sorted by model distance: nonbonded pdb=" OH TYR D 217 " pdb=" OD2 ASP D 225 " model vdw 2.244 3.040 nonbonded pdb=" OG1 THR D 55 " pdb=" ND2 ASN D 58 " model vdw 2.258 3.120 nonbonded pdb=" O ASP D 499 " pdb=" OG SER D 502 " model vdw 2.275 3.040 nonbonded pdb=" O ILE D 151 " pdb=" OG SER D 155 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR A 499 " pdb=" OH TYR D 41 " model vdw 2.281 3.040 ... (remaining 50974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.860 Find NCS groups from input model: 0.100 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6863 Z= 0.156 Angle : 0.611 10.924 9356 Z= 0.288 Chirality : 0.048 0.590 1013 Planarity : 0.003 0.040 1180 Dihedral : 15.767 109.087 2709 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.11 (0.32), residues: 790 helix: 2.27 (0.27), residues: 389 sheet: 0.99 (0.87), residues: 44 loop : -1.11 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 566 HIS 0.003 0.001 HIS D 540 PHE 0.011 0.001 PHE D 369 TYR 0.007 0.001 TYR D 183 ARG 0.001 0.000 ARG D 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00892 ( 8) link_NAG-ASN : angle 4.01767 ( 24) link_ALPHA1-6 : bond 0.00307 ( 1) link_ALPHA1-6 : angle 1.67743 ( 3) link_BETA1-4 : bond 0.00401 ( 5) link_BETA1-4 : angle 1.84559 ( 15) link_ALPHA1-3 : bond 0.00119 ( 1) link_ALPHA1-3 : angle 1.95056 ( 3) hydrogen bonds : bond 0.14815 ( 302) hydrogen bonds : angle 5.25394 ( 867) SS BOND : bond 0.00063 ( 7) SS BOND : angle 0.45246 ( 14) covalent geometry : bond 0.00306 ( 6841) covalent geometry : angle 0.57094 ( 9297) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 378 LYS cc_start: 0.6951 (tppp) cc_final: 0.6666 (mmmt) REVERT: A 380 TYR cc_start: 0.8020 (m-80) cc_final: 0.7601 (m-80) REVERT: A 383 SER cc_start: 0.7511 (m) cc_final: 0.7191 (p) REVERT: A 444 LYS cc_start: 0.7176 (mtmt) cc_final: 0.6940 (mtpt) REVERT: A 467 ASP cc_start: 0.7779 (t0) cc_final: 0.7530 (t0) REVERT: D 197 GLU cc_start: 0.7506 (mp0) cc_final: 0.6728 (mp0) REVERT: D 329 GLU cc_start: 0.6533 (tp30) cc_final: 0.6294 (mt-10) REVERT: D 341 LYS cc_start: 0.7752 (mtmt) cc_final: 0.7203 (mtpp) REVERT: D 435 GLU cc_start: 0.6131 (mm-30) cc_final: 0.5844 (pt0) REVERT: D 474 MET cc_start: 0.6375 (mmp) cc_final: 0.5727 (mmp) REVERT: D 596 LYS cc_start: 0.6949 (mtmt) cc_final: 0.6622 (mtmm) REVERT: D 597 ASP cc_start: 0.7716 (t0) cc_final: 0.7453 (t70) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1983 time to fit residues: 41.7502 Evaluate side-chains 100 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.0470 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 58 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.151063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122012 restraints weight = 8657.409| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.54 r_work: 0.3291 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6863 Z= 0.127 Angle : 0.593 11.629 9356 Z= 0.292 Chirality : 0.046 0.344 1013 Planarity : 0.004 0.036 1180 Dihedral : 10.569 78.986 1168 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.81 % Favored : 95.06 % Rotamer: Outliers : 1.72 % Allowed : 8.17 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.32), residues: 790 helix: 2.22 (0.28), residues: 394 sheet: 0.61 (0.80), residues: 44 loop : -1.23 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.004 0.001 HIS D 374 PHE 0.013 0.001 PHE A 392 TYR 0.015 0.001 TYR A 494 ARG 0.003 0.000 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00669 ( 8) link_NAG-ASN : angle 3.18492 ( 24) link_ALPHA1-6 : bond 0.00516 ( 1) link_ALPHA1-6 : angle 1.54275 ( 3) link_BETA1-4 : bond 0.00433 ( 5) link_BETA1-4 : angle 2.12248 ( 15) link_ALPHA1-3 : bond 0.00715 ( 1) link_ALPHA1-3 : angle 2.29705 ( 3) hydrogen bonds : bond 0.05403 ( 302) hydrogen bonds : angle 4.24917 ( 867) SS BOND : bond 0.00318 ( 7) SS BOND : angle 1.59296 ( 14) covalent geometry : bond 0.00268 ( 6841) covalent geometry : angle 0.56037 ( 9297) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: D 197 GLU cc_start: 0.7818 (mp0) cc_final: 0.7399 (mp0) REVERT: D 287 GLN cc_start: 0.7872 (mp10) cc_final: 0.7669 (mp10) REVERT: D 341 LYS cc_start: 0.8267 (mtmt) cc_final: 0.7865 (mtpp) REVERT: D 416 LYS cc_start: 0.7304 (ttmm) cc_final: 0.7099 (ttpp) REVERT: D 435 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7014 (pt0) REVERT: D 597 ASP cc_start: 0.8449 (t0) cc_final: 0.8247 (t70) outliers start: 12 outliers final: 8 residues processed: 110 average time/residue: 0.1824 time to fit residues: 27.0669 Evaluate side-chains 98 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 507 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.0020 chunk 65 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 0.0000 chunk 66 optimal weight: 4.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.150319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122676 restraints weight = 8637.354| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.40 r_work: 0.3323 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6863 Z= 0.109 Angle : 0.534 9.078 9356 Z= 0.262 Chirality : 0.044 0.322 1013 Planarity : 0.004 0.036 1180 Dihedral : 8.642 70.662 1168 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.81 % Favored : 95.06 % Rotamer: Outliers : 2.01 % Allowed : 10.32 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.31), residues: 790 helix: 2.18 (0.28), residues: 397 sheet: 0.64 (0.79), residues: 44 loop : -1.21 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS D 374 PHE 0.011 0.001 PHE D 369 TYR 0.013 0.001 TYR D 183 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00978 ( 8) link_NAG-ASN : angle 3.40150 ( 24) link_ALPHA1-6 : bond 0.00801 ( 1) link_ALPHA1-6 : angle 1.58028 ( 3) link_BETA1-4 : bond 0.00489 ( 5) link_BETA1-4 : angle 1.92600 ( 15) link_ALPHA1-3 : bond 0.00969 ( 1) link_ALPHA1-3 : angle 1.57547 ( 3) hydrogen bonds : bond 0.04771 ( 302) hydrogen bonds : angle 4.12032 ( 867) SS BOND : bond 0.00645 ( 7) SS BOND : angle 1.66566 ( 14) covalent geometry : bond 0.00218 ( 6841) covalent geometry : angle 0.49578 ( 9297) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8765 (p0) cc_final: 0.8398 (p0) REVERT: D 87 GLU cc_start: 0.7511 (mp0) cc_final: 0.7249 (pm20) REVERT: D 201 ASP cc_start: 0.8564 (t0) cc_final: 0.7890 (m-30) REVERT: D 341 LYS cc_start: 0.8395 (mtmt) cc_final: 0.7930 (mtpp) REVERT: D 534 LYS cc_start: 0.7580 (mmpt) cc_final: 0.7373 (mmpt) outliers start: 14 outliers final: 9 residues processed: 102 average time/residue: 0.1792 time to fit residues: 24.8766 Evaluate side-chains 98 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 507 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.148219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119304 restraints weight = 8771.147| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.51 r_work: 0.3269 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6863 Z= 0.133 Angle : 0.556 9.344 9356 Z= 0.275 Chirality : 0.045 0.309 1013 Planarity : 0.004 0.039 1180 Dihedral : 7.693 64.762 1168 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.06 % Favored : 94.81 % Rotamer: Outliers : 2.01 % Allowed : 12.46 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.31), residues: 790 helix: 2.12 (0.28), residues: 398 sheet: 0.58 (0.78), residues: 44 loop : -1.26 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.006 0.001 HIS D 374 PHE 0.014 0.001 PHE D 369 TYR 0.017 0.001 TYR D 183 ARG 0.003 0.000 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00753 ( 8) link_NAG-ASN : angle 3.16677 ( 24) link_ALPHA1-6 : bond 0.00841 ( 1) link_ALPHA1-6 : angle 1.49963 ( 3) link_BETA1-4 : bond 0.00511 ( 5) link_BETA1-4 : angle 1.85488 ( 15) link_ALPHA1-3 : bond 0.00924 ( 1) link_ALPHA1-3 : angle 1.69987 ( 3) hydrogen bonds : bond 0.05547 ( 302) hydrogen bonds : angle 4.07581 ( 867) SS BOND : bond 0.00576 ( 7) SS BOND : angle 1.52011 ( 14) covalent geometry : bond 0.00295 ( 6841) covalent geometry : angle 0.52352 ( 9297) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.7694 (ttm-80) REVERT: A 420 ASP cc_start: 0.8664 (p0) cc_final: 0.8241 (p0) REVERT: D 87 GLU cc_start: 0.7385 (mp0) cc_final: 0.7149 (pm20) REVERT: D 118 THR cc_start: 0.7906 (m) cc_final: 0.7576 (p) REVERT: D 201 ASP cc_start: 0.8549 (t0) cc_final: 0.8338 (t0) REVERT: D 215 TYR cc_start: 0.7782 (m-80) cc_final: 0.7563 (m-80) REVERT: D 341 LYS cc_start: 0.8297 (mtmt) cc_final: 0.7837 (mtpp) REVERT: D 397 ASN cc_start: 0.8027 (p0) cc_final: 0.7790 (p0) outliers start: 14 outliers final: 9 residues processed: 99 average time/residue: 0.1842 time to fit residues: 24.7927 Evaluate side-chains 94 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 507 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.0870 chunk 68 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.143948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.115242 restraints weight = 8735.195| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.47 r_work: 0.3238 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6863 Z= 0.162 Angle : 0.589 9.895 9356 Z= 0.296 Chirality : 0.046 0.304 1013 Planarity : 0.004 0.046 1180 Dihedral : 7.518 60.382 1168 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.70 % Favored : 94.18 % Rotamer: Outliers : 1.86 % Allowed : 14.04 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.70 (0.31), residues: 790 helix: 2.00 (0.28), residues: 397 sheet: 0.47 (0.78), residues: 44 loop : -1.44 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.007 0.002 HIS D 374 PHE 0.015 0.002 PHE D 369 TYR 0.021 0.002 TYR D 381 ARG 0.004 0.000 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00862 ( 8) link_NAG-ASN : angle 3.39589 ( 24) link_ALPHA1-6 : bond 0.00823 ( 1) link_ALPHA1-6 : angle 1.38847 ( 3) link_BETA1-4 : bond 0.00467 ( 5) link_BETA1-4 : angle 1.68938 ( 15) link_ALPHA1-3 : bond 0.00892 ( 1) link_ALPHA1-3 : angle 1.60088 ( 3) hydrogen bonds : bond 0.06413 ( 302) hydrogen bonds : angle 4.16344 ( 867) SS BOND : bond 0.00589 ( 7) SS BOND : angle 1.63656 ( 14) covalent geometry : bond 0.00376 ( 6841) covalent geometry : angle 0.55638 ( 9297) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7945 (ttm-80) REVERT: A 420 ASP cc_start: 0.8753 (p0) cc_final: 0.8337 (p0) REVERT: A 481 LYS cc_start: 0.7667 (ttmt) cc_final: 0.7101 (tptp) REVERT: D 201 ASP cc_start: 0.8770 (t0) cc_final: 0.8463 (t0) REVERT: D 215 TYR cc_start: 0.8043 (m-80) cc_final: 0.7831 (m-80) REVERT: D 341 LYS cc_start: 0.8377 (mtmt) cc_final: 0.7855 (mtpp) outliers start: 13 outliers final: 12 residues processed: 95 average time/residue: 0.1901 time to fit residues: 24.1912 Evaluate side-chains 95 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 507 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.146275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117964 restraints weight = 8784.925| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.39 r_work: 0.3221 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6863 Z= 0.126 Angle : 0.555 9.070 9356 Z= 0.273 Chirality : 0.045 0.299 1013 Planarity : 0.004 0.048 1180 Dihedral : 7.150 55.865 1168 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.57 % Favored : 94.30 % Rotamer: Outliers : 1.86 % Allowed : 14.76 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.31), residues: 790 helix: 1.99 (0.28), residues: 399 sheet: 0.64 (0.80), residues: 42 loop : -1.38 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS D 374 PHE 0.013 0.001 PHE D 369 TYR 0.016 0.001 TYR D 183 ARG 0.002 0.000 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00980 ( 8) link_NAG-ASN : angle 3.33462 ( 24) link_ALPHA1-6 : bond 0.01006 ( 1) link_ALPHA1-6 : angle 1.39240 ( 3) link_BETA1-4 : bond 0.00459 ( 5) link_BETA1-4 : angle 1.61806 ( 15) link_ALPHA1-3 : bond 0.00929 ( 1) link_ALPHA1-3 : angle 1.60779 ( 3) hydrogen bonds : bond 0.05487 ( 302) hydrogen bonds : angle 4.11425 ( 867) SS BOND : bond 0.00609 ( 7) SS BOND : angle 1.52450 ( 14) covalent geometry : bond 0.00271 ( 6841) covalent geometry : angle 0.52208 ( 9297) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7837 (ttm-80) REVERT: A 420 ASP cc_start: 0.8643 (p0) cc_final: 0.8257 (p0) REVERT: A 481 LYS cc_start: 0.7629 (ttmt) cc_final: 0.6986 (tptp) REVERT: D 118 THR cc_start: 0.7446 (m) cc_final: 0.7155 (p) REVERT: D 201 ASP cc_start: 0.8620 (t0) cc_final: 0.8313 (t0) REVERT: D 255 TYR cc_start: 0.7744 (m-80) cc_final: 0.7417 (m-10) REVERT: D 341 LYS cc_start: 0.8297 (mtmt) cc_final: 0.7696 (mtpp) REVERT: D 383 MET cc_start: 0.8332 (mtp) cc_final: 0.7850 (mtp) REVERT: D 397 ASN cc_start: 0.8166 (p0) cc_final: 0.7879 (p0) outliers start: 13 outliers final: 11 residues processed: 94 average time/residue: 0.2104 time to fit residues: 26.1685 Evaluate side-chains 94 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 507 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.147476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118994 restraints weight = 8741.218| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.42 r_work: 0.3277 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6863 Z= 0.130 Angle : 0.557 9.387 9356 Z= 0.275 Chirality : 0.044 0.304 1013 Planarity : 0.004 0.048 1180 Dihedral : 6.834 55.908 1168 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.82 % Favored : 94.05 % Rotamer: Outliers : 1.72 % Allowed : 15.62 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.31), residues: 790 helix: 1.97 (0.28), residues: 400 sheet: 0.59 (0.79), residues: 42 loop : -1.38 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS D 374 PHE 0.013 0.001 PHE D 369 TYR 0.017 0.001 TYR D 183 ARG 0.002 0.000 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00779 ( 8) link_NAG-ASN : angle 3.21025 ( 24) link_ALPHA1-6 : bond 0.01006 ( 1) link_ALPHA1-6 : angle 1.13543 ( 3) link_BETA1-4 : bond 0.00458 ( 5) link_BETA1-4 : angle 1.50212 ( 15) link_ALPHA1-3 : bond 0.00945 ( 1) link_ALPHA1-3 : angle 1.55918 ( 3) hydrogen bonds : bond 0.05589 ( 302) hydrogen bonds : angle 4.10993 ( 867) SS BOND : bond 0.00585 ( 7) SS BOND : angle 1.52767 ( 14) covalent geometry : bond 0.00286 ( 6841) covalent geometry : angle 0.52709 ( 9297) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7913 (ttm-80) REVERT: A 420 ASP cc_start: 0.8734 (p0) cc_final: 0.8337 (p0) REVERT: A 481 LYS cc_start: 0.7626 (ttmt) cc_final: 0.7191 (tptp) REVERT: D 201 ASP cc_start: 0.8730 (t0) cc_final: 0.8449 (t0) REVERT: D 255 TYR cc_start: 0.7840 (m-80) cc_final: 0.7510 (m-10) REVERT: D 341 LYS cc_start: 0.8365 (mtmt) cc_final: 0.7851 (mtpp) REVERT: D 383 MET cc_start: 0.8649 (mtp) cc_final: 0.8228 (mtp) REVERT: D 397 ASN cc_start: 0.8280 (p0) cc_final: 0.8001 (p0) REVERT: D 536 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7641 (mt-10) outliers start: 12 outliers final: 11 residues processed: 91 average time/residue: 0.1884 time to fit residues: 23.2585 Evaluate side-chains 94 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 536 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.0570 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118699 restraints weight = 8784.312| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.43 r_work: 0.3274 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6863 Z= 0.130 Angle : 0.553 9.275 9356 Z= 0.273 Chirality : 0.044 0.304 1013 Planarity : 0.004 0.048 1180 Dihedral : 6.614 55.757 1168 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.32 % Favored : 94.56 % Rotamer: Outliers : 2.01 % Allowed : 15.62 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.31), residues: 790 helix: 1.95 (0.28), residues: 400 sheet: 0.55 (0.79), residues: 42 loop : -1.36 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS D 374 PHE 0.013 0.001 PHE D 369 TYR 0.017 0.001 TYR D 183 ARG 0.002 0.000 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00731 ( 8) link_NAG-ASN : angle 3.12304 ( 24) link_ALPHA1-6 : bond 0.01085 ( 1) link_ALPHA1-6 : angle 0.99251 ( 3) link_BETA1-4 : bond 0.00470 ( 5) link_BETA1-4 : angle 1.43082 ( 15) link_ALPHA1-3 : bond 0.00912 ( 1) link_ALPHA1-3 : angle 1.52000 ( 3) hydrogen bonds : bond 0.05543 ( 302) hydrogen bonds : angle 4.11044 ( 867) SS BOND : bond 0.00578 ( 7) SS BOND : angle 1.52022 ( 14) covalent geometry : bond 0.00287 ( 6841) covalent geometry : angle 0.52398 ( 9297) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8239 (ttm-80) cc_final: 0.7939 (ttm-80) REVERT: A 420 ASP cc_start: 0.8729 (p0) cc_final: 0.8328 (p0) REVERT: A 481 LYS cc_start: 0.7656 (ttmt) cc_final: 0.7185 (tptp) REVERT: D 118 THR cc_start: 0.7850 (m) cc_final: 0.7510 (p) REVERT: D 201 ASP cc_start: 0.8736 (t0) cc_final: 0.8452 (t0) REVERT: D 255 TYR cc_start: 0.7849 (m-80) cc_final: 0.7515 (m-10) REVERT: D 341 LYS cc_start: 0.8366 (mtmt) cc_final: 0.7875 (mtpp) REVERT: D 383 MET cc_start: 0.8656 (mtp) cc_final: 0.8247 (mtp) REVERT: D 397 ASN cc_start: 0.8297 (p0) cc_final: 0.8003 (p0) REVERT: D 536 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7639 (mt-10) outliers start: 14 outliers final: 12 residues processed: 91 average time/residue: 0.2054 time to fit residues: 25.0666 Evaluate side-chains 95 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 536 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.0070 chunk 58 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.150804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122303 restraints weight = 8815.861| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.44 r_work: 0.3323 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6863 Z= 0.104 Angle : 0.517 8.553 9356 Z= 0.252 Chirality : 0.042 0.303 1013 Planarity : 0.004 0.047 1180 Dihedral : 6.138 59.270 1168 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.32 % Favored : 94.56 % Rotamer: Outliers : 2.01 % Allowed : 15.33 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.83 (0.31), residues: 790 helix: 2.05 (0.28), residues: 395 sheet: 0.60 (0.79), residues: 42 loop : -1.27 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.003 0.001 HIS D 540 PHE 0.011 0.001 PHE D 369 TYR 0.014 0.001 TYR D 183 ARG 0.001 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00744 ( 8) link_NAG-ASN : angle 2.92623 ( 24) link_ALPHA1-6 : bond 0.01237 ( 1) link_ALPHA1-6 : angle 1.04269 ( 3) link_BETA1-4 : bond 0.00496 ( 5) link_BETA1-4 : angle 1.29570 ( 15) link_ALPHA1-3 : bond 0.00915 ( 1) link_ALPHA1-3 : angle 1.42340 ( 3) hydrogen bonds : bond 0.04558 ( 302) hydrogen bonds : angle 4.06074 ( 867) SS BOND : bond 0.00545 ( 7) SS BOND : angle 1.30355 ( 14) covalent geometry : bond 0.00212 ( 6841) covalent geometry : angle 0.49018 ( 9297) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.7970 (ttm-80) REVERT: A 420 ASP cc_start: 0.8657 (p0) cc_final: 0.8300 (p0) REVERT: A 481 LYS cc_start: 0.7535 (ttmt) cc_final: 0.7037 (tptp) REVERT: D 118 THR cc_start: 0.7936 (m) cc_final: 0.7597 (p) REVERT: D 201 ASP cc_start: 0.8679 (t0) cc_final: 0.8424 (t0) REVERT: D 255 TYR cc_start: 0.7816 (m-80) cc_final: 0.7530 (m-10) REVERT: D 341 LYS cc_start: 0.8365 (mtmt) cc_final: 0.7874 (mtpp) REVERT: D 383 MET cc_start: 0.8470 (mtp) cc_final: 0.8098 (mtp) REVERT: D 536 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7577 (mt-10) outliers start: 14 outliers final: 12 residues processed: 97 average time/residue: 0.1903 time to fit residues: 24.8692 Evaluate side-chains 98 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 536 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.147718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119202 restraints weight = 8900.989| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.45 r_work: 0.3280 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6863 Z= 0.130 Angle : 0.547 8.721 9356 Z= 0.272 Chirality : 0.043 0.298 1013 Planarity : 0.004 0.048 1180 Dihedral : 6.117 59.608 1168 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.44 % Favored : 94.43 % Rotamer: Outliers : 2.01 % Allowed : 16.05 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.31), residues: 790 helix: 2.05 (0.28), residues: 395 sheet: 0.59 (0.79), residues: 42 loop : -1.32 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS D 374 PHE 0.013 0.001 PHE D 369 TYR 0.017 0.001 TYR D 183 ARG 0.002 0.000 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00711 ( 8) link_NAG-ASN : angle 3.00782 ( 24) link_ALPHA1-6 : bond 0.01212 ( 1) link_ALPHA1-6 : angle 1.27358 ( 3) link_BETA1-4 : bond 0.00455 ( 5) link_BETA1-4 : angle 1.30836 ( 15) link_ALPHA1-3 : bond 0.00876 ( 1) link_ALPHA1-3 : angle 1.46422 ( 3) hydrogen bonds : bond 0.05456 ( 302) hydrogen bonds : angle 4.07959 ( 867) SS BOND : bond 0.00553 ( 7) SS BOND : angle 1.41510 ( 14) covalent geometry : bond 0.00286 ( 6841) covalent geometry : angle 0.52068 ( 9297) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8247 (ttm-80) cc_final: 0.7968 (ttm-80) REVERT: A 420 ASP cc_start: 0.8711 (p0) cc_final: 0.8392 (p0) REVERT: A 441 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7466 (mt) REVERT: A 481 LYS cc_start: 0.7575 (ttmt) cc_final: 0.7063 (tptp) REVERT: D 118 THR cc_start: 0.7950 (m) cc_final: 0.7610 (p) REVERT: D 201 ASP cc_start: 0.8731 (t0) cc_final: 0.8456 (t0) REVERT: D 255 TYR cc_start: 0.7854 (m-80) cc_final: 0.7561 (m-10) REVERT: D 341 LYS cc_start: 0.8367 (mtmt) cc_final: 0.7890 (mtpp) REVERT: D 383 MET cc_start: 0.8627 (mtp) cc_final: 0.8202 (mtp) REVERT: D 536 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7648 (mt-10) outliers start: 14 outliers final: 11 residues processed: 93 average time/residue: 0.1988 time to fit residues: 24.8969 Evaluate side-chains 94 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 536 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119961 restraints weight = 8845.432| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.43 r_work: 0.3291 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6863 Z= 0.120 Angle : 0.537 8.621 9356 Z= 0.266 Chirality : 0.043 0.290 1013 Planarity : 0.004 0.048 1180 Dihedral : 6.009 58.431 1168 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.57 % Favored : 94.30 % Rotamer: Outliers : 2.01 % Allowed : 15.47 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.31), residues: 790 helix: 2.04 (0.28), residues: 394 sheet: 0.55 (0.79), residues: 42 loop : -1.33 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS D 374 PHE 0.012 0.001 PHE D 369 TYR 0.016 0.001 TYR D 183 ARG 0.002 0.000 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00711 ( 8) link_NAG-ASN : angle 2.96620 ( 24) link_ALPHA1-6 : bond 0.01225 ( 1) link_ALPHA1-6 : angle 1.27508 ( 3) link_BETA1-4 : bond 0.00473 ( 5) link_BETA1-4 : angle 1.28157 ( 15) link_ALPHA1-3 : bond 0.00896 ( 1) link_ALPHA1-3 : angle 1.45539 ( 3) hydrogen bonds : bond 0.05200 ( 302) hydrogen bonds : angle 4.08853 ( 867) SS BOND : bond 0.00554 ( 7) SS BOND : angle 1.37740 ( 14) covalent geometry : bond 0.00259 ( 6841) covalent geometry : angle 0.51054 ( 9297) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3870.07 seconds wall clock time: 67 minutes 33.66 seconds (4053.66 seconds total)