Starting phenix.real_space_refine on Mon Jul 28 21:47:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xv1_38689/07_2025/8xv1_38689.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xv1_38689/07_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_38689/07_2025/8xv1_38689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xv1_38689/07_2025/8xv1_38689.map" model { file = "/net/cci-nas-00/data/ceres_data/8xv1_38689/07_2025/8xv1_38689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xv1_38689/07_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-5711/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: 5.34, per 1000 atoms: 0.80 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: 1.97 Conformation dependent library (CDL) restraints added in 899.4 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: 0.67 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: 1.85 Time building geometry restraints manager: 2.30 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: 14.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.790 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.020 ------------------------------------------------------------------------------- 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 : 0.723 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: 0.2473 time to fit residues: 52.6216 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 : 0.709 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122022 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 : 0.750 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: 0.7670 (mp10) REVERT: D 341 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7865 (mtpp) REVERT: D 416 LYS cc_start: 0.7303 (ttmm) cc_final: 0.7099 (ttpp) REVERT: D 435 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7013 (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: 0.1870 time to fit residues: 27.7427 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 : 0.768 ------------------------------------------------------------------------------- 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: 0.9990 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 0.0000 chunk 66 optimal weight: 3.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.149691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121082 restraints weight = 8662.747| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.46 r_work: 0.3297 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6863 Z= 0.119 Angle : 0.550 9.317 9356 Z= 0.271 Chirality : 0.045 0.340 1013 Planarity : 0.004 0.036 1180 Dihedral : 8.941 72.421 1168 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.06 % Favored : 94.81 % Rotamer: Outliers : 1.86 % Allowed : 10.03 % Favored : 88.11 % 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: 0.94 (0.31), residues: 790 helix: 2.18 (0.28), residues: 395 sheet: 0.60 (0.79), residues: 44 loop : -1.29 (0.32), residues: 351 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 0.012 0.001 PHE D 369 TYR 0.014 0.001 TYR D 183 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00958 ( 8) link_NAG-ASN : angle 3.36146 ( 24) link_ALPHA1-6 : bond 0.00777 ( 1) link_ALPHA1-6 : angle 1.64977 ( 3) link_BETA1-4 : bond 0.00412 ( 5) link_BETA1-4 : angle 1.93117 ( 15) link_ALPHA1-3 : bond 0.00937 ( 1) link_ALPHA1-3 : angle 1.61026 ( 3) hydrogen bonds : bond 0.05191 ( 302) hydrogen bonds : angle 4.14005 ( 867) SS BOND : bond 0.00635 ( 7) SS BOND : angle 1.62003 ( 14) covalent geometry : bond 0.00253 ( 6841) covalent geometry : angle 0.51338 ( 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 105 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: D 87 GLU cc_start: 0.7527 (mp0) cc_final: 0.7296 (pm20) REVERT: D 118 THR cc_start: 0.7828 (m) cc_final: 0.7508 (p) REVERT: D 201 ASP cc_start: 0.8619 (t0) cc_final: 0.7778 (t70) REVERT: D 341 LYS cc_start: 0.8410 (mtmt) cc_final: 0.7948 (mtpp) REVERT: D 383 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8032 (mtp) REVERT: D 597 ASP cc_start: 0.8573 (t0) cc_final: 0.8365 (t70) outliers start: 13 outliers final: 9 residues processed: 98 average time/residue: 0.1921 time to fit residues: 25.5867 Evaluate side-chains 97 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 383 MET 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: 3.9990 chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116951 restraints weight = 8785.148| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.47 r_work: 0.3240 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6863 Z= 0.151 Angle : 0.582 9.815 9356 Z= 0.290 Chirality : 0.046 0.313 1013 Planarity : 0.004 0.041 1180 Dihedral : 8.018 66.784 1168 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.06 % Favored : 94.81 % Rotamer: Outliers : 2.01 % Allowed : 12.89 % Favored : 85.10 % 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: 0.78 (0.31), residues: 790 helix: 2.04 (0.28), residues: 397 sheet: 0.44 (0.78), residues: 44 loop : -1.35 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.007 0.001 HIS D 374 PHE 0.014 0.002 PHE D 369 TYR 0.018 0.002 TYR A 494 ARG 0.003 0.000 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00782 ( 8) link_NAG-ASN : angle 3.22872 ( 24) link_ALPHA1-6 : bond 0.00886 ( 1) link_ALPHA1-6 : angle 1.54632 ( 3) link_BETA1-4 : bond 0.00421 ( 5) link_BETA1-4 : angle 1.92559 ( 15) link_ALPHA1-3 : bond 0.00903 ( 1) link_ALPHA1-3 : angle 1.68268 ( 3) hydrogen bonds : bond 0.06108 ( 302) hydrogen bonds : angle 4.13169 ( 867) SS BOND : bond 0.00595 ( 7) SS BOND : angle 1.62504 ( 14) covalent geometry : bond 0.00343 ( 6841) covalent geometry : angle 0.55007 ( 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 102 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.7891 (ttm-80) REVERT: A 420 ASP cc_start: 0.8768 (p0) cc_final: 0.8340 (p0) REVERT: A 481 LYS cc_start: 0.7639 (ttmt) cc_final: 0.7109 (tptp) REVERT: D 201 ASP cc_start: 0.8763 (t0) cc_final: 0.8507 (t0) REVERT: D 215 TYR cc_start: 0.7959 (m-80) cc_final: 0.7717 (m-80) REVERT: D 341 LYS cc_start: 0.8396 (mtmt) cc_final: 0.7882 (mtpp) REVERT: D 383 MET cc_start: 0.8657 (mtp) cc_final: 0.8445 (mtp) REVERT: D 597 ASP cc_start: 0.8593 (t0) cc_final: 0.8390 (t70) outliers start: 14 outliers final: 10 residues processed: 96 average time/residue: 0.1867 time to fit residues: 24.3011 Evaluate side-chains 94 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.3980 chunk 68 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 0.0000 chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.147566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119705 restraints weight = 8755.496| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.40 r_work: 0.3252 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2189 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= 0.132 Angle : 0.555 9.253 9356 Z= 0.275 Chirality : 0.045 0.304 1013 Planarity : 0.004 0.045 1180 Dihedral : 7.552 60.929 1168 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.57 % Favored : 94.30 % Rotamer: Outliers : 2.15 % Allowed : 13.75 % 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: 0.75 (0.31), residues: 790 helix: 2.03 (0.28), residues: 397 sheet: 0.44 (0.78), residues: 44 loop : -1.39 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.005 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 0.01006 ( 8) link_NAG-ASN : angle 3.49095 ( 24) link_ALPHA1-6 : bond 0.00941 ( 1) link_ALPHA1-6 : angle 1.46576 ( 3) link_BETA1-4 : bond 0.00472 ( 5) link_BETA1-4 : angle 1.70001 ( 15) link_ALPHA1-3 : bond 0.00942 ( 1) link_ALPHA1-3 : angle 1.60662 ( 3) hydrogen bonds : bond 0.05608 ( 302) hydrogen bonds : angle 4.12900 ( 867) SS BOND : bond 0.00586 ( 7) SS BOND : angle 1.46951 ( 14) covalent geometry : bond 0.00292 ( 6841) covalent geometry : angle 0.51834 ( 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 103 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8242 (ttm-80) cc_final: 0.7973 (ttm-80) REVERT: A 420 ASP cc_start: 0.8726 (p0) cc_final: 0.8319 (p0) REVERT: A 481 LYS cc_start: 0.7630 (ttmt) cc_final: 0.7089 (tptp) REVERT: D 118 THR cc_start: 0.7926 (m) cc_final: 0.7596 (p) REVERT: D 201 ASP cc_start: 0.8754 (t0) cc_final: 0.8483 (t0) REVERT: D 215 TYR cc_start: 0.7978 (m-80) cc_final: 0.7665 (m-80) REVERT: D 341 LYS cc_start: 0.8398 (mtmt) cc_final: 0.7870 (mtpp) REVERT: D 383 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8202 (mtp) REVERT: D 597 ASP cc_start: 0.8577 (t0) cc_final: 0.8366 (t70) outliers start: 15 outliers final: 12 residues processed: 96 average time/residue: 0.1950 time to fit residues: 25.3023 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 : 0.745 ------------------------------------------------------------------------------- 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 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 334 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 383 MET 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: 0.8980 chunk 68 optimal weight: 3.9990 chunk 2 optimal weight: 0.0010 chunk 67 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 75 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.147646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119090 restraints weight = 8722.322| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.40 r_work: 0.3256 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6863 Z= 0.109 Angle : 0.526 9.101 9356 Z= 0.259 Chirality : 0.044 0.322 1013 Planarity : 0.004 0.046 1180 Dihedral : 6.984 55.478 1168 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.32 % Favored : 94.56 % Rotamer: Outliers : 2.01 % Allowed : 14.04 % Favored : 83.95 % 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: 0.85 (0.31), residues: 790 helix: 2.01 (0.28), residues: 401 sheet: 0.62 (0.79), residues: 42 loop : -1.24 (0.33), residues: 347 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 0.015 0.001 TYR D 183 ARG 0.001 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.01091 ( 8) link_NAG-ASN : angle 3.06836 ( 24) link_ALPHA1-6 : bond 0.00998 ( 1) link_ALPHA1-6 : angle 1.40855 ( 3) link_BETA1-4 : bond 0.00529 ( 5) link_BETA1-4 : angle 1.51991 ( 15) link_ALPHA1-3 : bond 0.00955 ( 1) link_ALPHA1-3 : angle 1.61096 ( 3) hydrogen bonds : bond 0.04816 ( 302) hydrogen bonds : angle 4.06873 ( 867) SS BOND : bond 0.00586 ( 7) SS BOND : angle 1.40504 ( 14) covalent geometry : bond 0.00221 ( 6841) covalent geometry : angle 0.49615 ( 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 102 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7832 (ttm-80) REVERT: A 420 ASP cc_start: 0.8621 (p0) cc_final: 0.8257 (p0) REVERT: A 481 LYS cc_start: 0.7623 (ttmt) cc_final: 0.6979 (tptp) REVERT: D 201 ASP cc_start: 0.8610 (t0) cc_final: 0.8342 (t0) REVERT: D 215 TYR cc_start: 0.7784 (m-80) cc_final: 0.7454 (m-80) REVERT: D 255 TYR cc_start: 0.7722 (m-80) cc_final: 0.7409 (m-10) REVERT: D 341 LYS cc_start: 0.8323 (mtmt) cc_final: 0.7741 (mtpp) REVERT: D 383 MET cc_start: 0.8175 (mtp) cc_final: 0.7722 (mtp) REVERT: D 597 ASP cc_start: 0.8419 (t0) cc_final: 0.8178 (t70) outliers start: 14 outliers final: 13 residues processed: 95 average time/residue: 0.1831 time to fit residues: 23.6048 Evaluate side-chains 99 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 87 GLU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 70 optimal weight: 0.0040 chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.0570 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 overall best weight: 0.4110 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.150096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121462 restraints weight = 8734.803| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.43 r_work: 0.3268 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6863 Z= 0.103 Angle : 0.507 8.484 9356 Z= 0.250 Chirality : 0.042 0.303 1013 Planarity : 0.004 0.046 1180 Dihedral : 6.306 55.321 1168 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.68 % Favored : 95.19 % Rotamer: Outliers : 1.43 % Allowed : 15.04 % Favored : 83.52 % 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: 0.92 (0.31), residues: 790 helix: 2.06 (0.28), residues: 401 sheet: 0.66 (0.78), residues: 42 loop : -1.20 (0.33), residues: 347 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 0.015 0.001 TYR D 183 ARG 0.001 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00796 ( 8) link_NAG-ASN : angle 2.96007 ( 24) link_ALPHA1-6 : bond 0.01075 ( 1) link_ALPHA1-6 : angle 1.03009 ( 3) link_BETA1-4 : bond 0.00519 ( 5) link_BETA1-4 : angle 1.37447 ( 15) link_ALPHA1-3 : bond 0.00978 ( 1) link_ALPHA1-3 : angle 1.52487 ( 3) hydrogen bonds : bond 0.04460 ( 302) hydrogen bonds : angle 4.02142 ( 867) SS BOND : bond 0.00507 ( 7) SS BOND : angle 1.25446 ( 14) covalent geometry : bond 0.00209 ( 6841) covalent geometry : angle 0.47874 ( 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 103 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7801 (ttm-80) REVERT: A 420 ASP cc_start: 0.8575 (p0) cc_final: 0.8310 (p0) REVERT: A 481 LYS cc_start: 0.7617 (ttmt) cc_final: 0.6956 (tptp) REVERT: D 114 LYS cc_start: 0.7324 (mtpt) cc_final: 0.6884 (mtpp) REVERT: D 118 THR cc_start: 0.7455 (m) cc_final: 0.7175 (p) REVERT: D 201 ASP cc_start: 0.8578 (t0) cc_final: 0.8329 (t0) REVERT: D 215 TYR cc_start: 0.7829 (m-80) cc_final: 0.7618 (m-80) REVERT: D 255 TYR cc_start: 0.7710 (m-80) cc_final: 0.7419 (m-10) REVERT: D 341 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7742 (mtpp) REVERT: D 597 ASP cc_start: 0.8359 (t0) cc_final: 0.7797 (m-30) outliers start: 10 outliers final: 10 residues processed: 98 average time/residue: 0.1973 time to fit residues: 25.7964 Evaluate side-chains 102 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 364 VAL Chi-restraints excluded: chain D residue 507 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.148851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120398 restraints weight = 8794.470| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.42 r_work: 0.3295 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6863 Z= 0.123 Angle : 0.533 8.633 9356 Z= 0.264 Chirality : 0.043 0.293 1013 Planarity : 0.004 0.047 1180 Dihedral : 6.205 57.398 1168 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.19 % Favored : 94.68 % Rotamer: Outliers : 1.86 % Allowed : 14.61 % Favored : 83.52 % 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: 0.89 (0.31), residues: 790 helix: 2.04 (0.28), residues: 401 sheet: 0.64 (0.78), residues: 42 loop : -1.24 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.00713 ( 8) link_NAG-ASN : angle 3.00285 ( 24) link_ALPHA1-6 : bond 0.01191 ( 1) link_ALPHA1-6 : angle 1.03924 ( 3) link_BETA1-4 : bond 0.00467 ( 5) link_BETA1-4 : angle 1.35752 ( 15) link_ALPHA1-3 : bond 0.00937 ( 1) link_ALPHA1-3 : angle 1.52157 ( 3) hydrogen bonds : bond 0.05201 ( 302) hydrogen bonds : angle 4.03295 ( 867) SS BOND : bond 0.00544 ( 7) SS BOND : angle 1.39632 ( 14) covalent geometry : bond 0.00270 ( 6841) covalent geometry : angle 0.50555 ( 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 103 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7907 (ttm-80) REVERT: A 420 ASP cc_start: 0.8706 (p0) cc_final: 0.8398 (p0) REVERT: A 481 LYS cc_start: 0.7588 (ttmt) cc_final: 0.7066 (tptp) REVERT: D 118 THR cc_start: 0.7980 (m) cc_final: 0.7631 (p) REVERT: D 201 ASP cc_start: 0.8744 (t0) cc_final: 0.8490 (t0) REVERT: D 255 TYR cc_start: 0.7823 (m-80) cc_final: 0.7537 (m-10) REVERT: D 341 LYS cc_start: 0.8404 (mtmt) cc_final: 0.7902 (mtpp) REVERT: D 597 ASP cc_start: 0.8563 (t0) cc_final: 0.8362 (t70) outliers start: 13 outliers final: 11 residues processed: 97 average time/residue: 0.1921 time to fit residues: 24.9844 Evaluate side-chains 99 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 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 364 VAL Chi-restraints excluded: chain D residue 507 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.148510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.120107 restraints weight = 8840.874| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.44 r_work: 0.3292 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6863 Z= 0.123 Angle : 0.529 8.580 9356 Z= 0.264 Chirality : 0.043 0.291 1013 Planarity : 0.004 0.047 1180 Dihedral : 6.098 57.862 1168 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.57 % Favored : 94.30 % Rotamer: Outliers : 2.01 % Allowed : 14.47 % Favored : 83.52 % 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: 0.83 (0.31), residues: 790 helix: 2.01 (0.28), residues: 400 sheet: 0.60 (0.78), residues: 42 loop : -1.27 (0.32), residues: 348 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 0.017 0.001 TYR D 183 ARG 0.002 0.000 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00726 ( 8) link_NAG-ASN : angle 2.98186 ( 24) link_ALPHA1-6 : bond 0.01238 ( 1) link_ALPHA1-6 : angle 1.16575 ( 3) link_BETA1-4 : bond 0.00470 ( 5) link_BETA1-4 : angle 1.31041 ( 15) link_ALPHA1-3 : bond 0.00937 ( 1) link_ALPHA1-3 : angle 1.48682 ( 3) hydrogen bonds : bond 0.05215 ( 302) hydrogen bonds : angle 4.06448 ( 867) SS BOND : bond 0.00542 ( 7) SS BOND : angle 1.38812 ( 14) covalent geometry : bond 0.00269 ( 6841) covalent geometry : angle 0.50177 ( 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 100 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7906 (ttm-80) REVERT: A 420 ASP cc_start: 0.8692 (p0) cc_final: 0.8322 (p0) REVERT: A 481 LYS cc_start: 0.7573 (ttmt) cc_final: 0.7048 (tptp) REVERT: D 201 ASP cc_start: 0.8762 (t0) cc_final: 0.8524 (t0) REVERT: D 255 TYR cc_start: 0.7833 (m-80) cc_final: 0.7529 (m-10) REVERT: D 341 LYS cc_start: 0.8406 (mtmt) cc_final: 0.7908 (mtpp) outliers start: 14 outliers final: 11 residues processed: 96 average time/residue: 0.1910 time to fit residues: 24.7015 Evaluate side-chains 97 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 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 364 VAL Chi-restraints excluded: chain D residue 507 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 49 optimal weight: 0.0970 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.149248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.120792 restraints weight = 8887.593| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.45 r_work: 0.3300 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6863 Z= 0.117 Angle : 0.540 8.524 9356 Z= 0.265 Chirality : 0.043 0.289 1013 Planarity : 0.004 0.046 1180 Dihedral : 5.988 59.587 1168 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.19 % Favored : 94.68 % Rotamer: Outliers : 1.86 % Allowed : 14.47 % Favored : 83.67 % 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: 0.86 (0.31), residues: 790 helix: 2.00 (0.28), residues: 401 sheet: 0.61 (0.78), residues: 42 loop : -1.21 (0.32), residues: 347 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 0.00722 ( 8) link_NAG-ASN : angle 2.94379 ( 24) link_ALPHA1-6 : bond 0.01238 ( 1) link_ALPHA1-6 : angle 1.23882 ( 3) link_BETA1-4 : bond 0.00477 ( 5) link_BETA1-4 : angle 1.28828 ( 15) link_ALPHA1-3 : bond 0.00894 ( 1) link_ALPHA1-3 : angle 1.44648 ( 3) hydrogen bonds : bond 0.05051 ( 302) hydrogen bonds : angle 4.05948 ( 867) SS BOND : bond 0.00563 ( 7) SS BOND : angle 1.39057 ( 14) covalent geometry : bond 0.00250 ( 6841) covalent geometry : angle 0.51374 ( 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 101 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7912 (ttm-80) REVERT: A 420 ASP cc_start: 0.8682 (p0) cc_final: 0.8375 (p0) REVERT: A 441 LEU cc_start: 0.7846 (mp) cc_final: 0.7486 (mt) REVERT: A 481 LYS cc_start: 0.7558 (ttmt) cc_final: 0.7031 (tptp) REVERT: D 118 THR cc_start: 0.7887 (m) cc_final: 0.7545 (p) REVERT: D 201 ASP cc_start: 0.8759 (t0) cc_final: 0.8521 (t0) REVERT: D 255 TYR cc_start: 0.7835 (m-80) cc_final: 0.7593 (m-10) REVERT: D 341 LYS cc_start: 0.8413 (mtmt) cc_final: 0.7920 (mtpp) outliers start: 13 outliers final: 12 residues processed: 98 average time/residue: 0.1931 time to fit residues: 25.4425 Evaluate side-chains 96 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 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 195 HIS Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 507 SER 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: 0.7980 chunk 54 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.147502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119076 restraints weight = 8864.093| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.44 r_work: 0.3278 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2515 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= 0.137 Angle : 0.571 9.006 9356 Z= 0.283 Chirality : 0.044 0.279 1013 Planarity : 0.004 0.047 1180 Dihedral : 6.025 57.382 1168 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.31 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: 0.79 (0.31), residues: 790 helix: 2.07 (0.28), residues: 394 sheet: 0.58 (0.78), residues: 42 loop : -1.36 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.006 0.001 HIS D 374 PHE 0.013 0.001 PHE D 369 TYR 0.017 0.002 TYR D 183 ARG 0.002 0.000 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00698 ( 8) link_NAG-ASN : angle 2.97109 ( 24) link_ALPHA1-6 : bond 0.01228 ( 1) link_ALPHA1-6 : angle 1.36334 ( 3) link_BETA1-4 : bond 0.00438 ( 5) link_BETA1-4 : angle 1.30131 ( 15) link_ALPHA1-3 : bond 0.00970 ( 1) link_ALPHA1-3 : angle 1.52269 ( 3) hydrogen bonds : bond 0.05577 ( 302) hydrogen bonds : angle 4.09950 ( 867) SS BOND : bond 0.00546 ( 7) SS BOND : angle 1.48621 ( 14) covalent geometry : bond 0.00306 ( 6841) covalent geometry : angle 0.54605 ( 9297) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4861.28 seconds wall clock time: 87 minutes 5.42 seconds (5225.42 seconds total)