Starting phenix.real_space_refine on Thu Jul 2 04:10:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dm8_27530/07_2026/8dm8_27530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm8_27530/07_2026/8dm8_27530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dm8_27530/07_2026/8dm8_27530.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dm8_27530/07_2026/8dm8_27530.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dm8_27530/07_2026/8dm8_27530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm8_27530/07_2026/8dm8_27530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dm8_27530/07_2026/8dm8_27530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm8_27530/07_2026/8dm8_27530.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4139 2.51 5 N 1087 2.21 5 O 1216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6479 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1604 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "D" Number of atoms: 4833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4833 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.47, per 1000 atoms: 0.23 Number of scatterers: 6479 At special positions: 0 Unit cell: (77, 86, 121, 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 1216 8.00 N 1087 7.00 C 4139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 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 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 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 NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 546 " Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 353.1 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: 39 helices and 7 sheets defined 56.5% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.909A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.409A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'D' and resid 21 through 52 removed outlier: 3.502A pdb=" N GLN D 34 " --> pdb=" O ASN D 30 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.739A pdb=" N GLU D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.670A pdb=" N SER D 106 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 128 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 193 removed outlier: 5.033A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.698A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (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 218 through 232 removed outlier: 3.709A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.613A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.525A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.622A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.848A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.613A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.419A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.672A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.663A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.307A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.128A 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 Processing helix chain 'D' and resid 588 through 598 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.549A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AA6, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.019A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.332A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 951 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: 0.71 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2071 1.35 - 1.47: 1789 1.47 - 1.60: 2744 1.60 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6662 Sorted by residual: bond pdb=" CG PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 1.503 1.589 -0.086 3.40e-02 8.65e+02 6.41e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.88e+00 bond pdb=" C1 NAG D 702 " pdb=" O5 NAG D 702 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.24e+00 bond pdb=" CB ASN A 439 " pdb=" CG ASN A 439 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.64e+00 bond pdb=" CB VAL D 573 " pdb=" CG2 VAL D 573 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.60e+00 ... (remaining 6657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 8688 2.10 - 4.19: 313 4.19 - 6.29: 37 6.29 - 8.38: 7 8.38 - 10.48: 3 Bond angle restraints: 9048 Sorted by residual: angle pdb=" N ALA A 372 " pdb=" CA ALA A 372 " pdb=" C ALA A 372 " ideal model delta sigma weight residual 109.81 120.01 -10.20 2.21e+00 2.05e-01 2.13e+01 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 124.88 -10.48 2.30e+00 1.89e-01 2.07e+01 angle pdb=" N VAL D 364 " pdb=" CA VAL D 364 " pdb=" C VAL D 364 " ideal model delta sigma weight residual 106.21 110.87 -4.66 1.07e+00 8.73e-01 1.90e+01 angle pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 112.00 105.96 6.04 1.40e+00 5.10e-01 1.86e+01 angle pdb=" C SER A 359 " pdb=" N ASN A 360 " pdb=" CA ASN A 360 " ideal model delta sigma weight residual 122.07 126.87 -4.80 1.43e+00 4.89e-01 1.13e+01 ... (remaining 9043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 3539 17.35 - 34.71: 319 34.71 - 52.06: 45 52.06 - 69.41: 11 69.41 - 86.77: 6 Dihedral angle restraints: 3920 sinusoidal: 1587 harmonic: 2333 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 55.15 37.85 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual 180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CG ARG D 245 " pdb=" CD ARG D 245 " pdb=" NE ARG D 245 " pdb=" CZ ARG D 245 " ideal model delta sinusoidal sigma weight residual 90.00 134.53 -44.53 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 3917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 641 0.051 - 0.103: 234 0.103 - 0.154: 56 0.154 - 0.205: 13 0.205 - 0.257: 3 Chirality restraints: 947 Sorted by residual: chirality pdb=" CB ILE D 291 " pdb=" CA ILE D 291 " pdb=" CG1 ILE D 291 " pdb=" CG2 ILE D 291 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB THR A 333 " pdb=" CA THR A 333 " pdb=" OG1 THR A 333 " pdb=" CG2 THR A 333 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ASN A 360 " pdb=" N ASN A 360 " pdb=" C ASN A 360 " pdb=" CB ASN A 360 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 944 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 36 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.60e+01 pdb=" C ALA D 36 " 0.069 2.00e-02 2.50e+03 pdb=" O ALA D 36 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU D 37 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 31 " -0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C ASN D 31 " 0.049 2.00e-02 2.50e+03 pdb=" O ASN D 31 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE D 32 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 499 " -0.044 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO D 500 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 500 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 500 " -0.037 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 1992 2.82 - 3.34: 5892 3.34 - 3.86: 11313 3.86 - 4.38: 13110 4.38 - 4.90: 22401 Nonbonded interactions: 54708 Sorted by model distance: nonbonded pdb=" O ILE D 151 " pdb=" OG SER D 155 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.315 3.040 nonbonded pdb=" OH TYR D 217 " pdb=" OD2 ASP D 225 " model vdw 2.339 3.040 nonbonded pdb=" OG1 THR A 500 " pdb=" OH TYR D 41 " model vdw 2.349 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.361 3.040 ... (remaining 54703 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: 0.010 Normalize map: mean=0, sd=1: 5.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.190 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 : 0.006 0.086 6671 Z= 0.270 Angle : 0.902 10.477 9069 Z= 0.500 Chirality : 0.058 0.257 947 Planarity : 0.007 0.065 1172 Dihedral : 13.412 86.766 2404 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.72 % Allowed : 1.74 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.26), residues: 790 helix: -0.44 (0.22), residues: 397 sheet: 0.63 (0.64), residues: 53 loop : -0.52 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 460 TYR 0.032 0.003 TYR D 385 PHE 0.024 0.003 PHE A 375 TRP 0.023 0.002 TRP D 163 HIS 0.006 0.002 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.27 ( 6662) covalent geometry : angle 0.89375 / 0.50 ( 9048) SS BOND : bond 0.00698 / 0.36 ( 6) SS BOND : angle 2.22262 / 1.36 ( 12) hydrogen bonds : bond 0.14393 / 8.91 ( 309) hydrogen bonds : angle 6.53863 / 4.63 ( 951) link_NAG-ASN : bond 0.00620 / 0.35 ( 3) link_NAG-ASN : angle 3.10303 / 1.47 ( 9) *********************** 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 162 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.7958 (m-40) cc_final: 0.7610 (m-40) REVERT: A 414 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8665 (mm-40) REVERT: D 113 ASN cc_start: 0.8620 (t0) cc_final: 0.8359 (t0) REVERT: D 145 GLU cc_start: 0.8438 (tp30) cc_final: 0.7852 (tp30) REVERT: D 347 THR cc_start: 0.8692 (m) cc_final: 0.8432 (p) REVERT: D 383 MET cc_start: 0.9163 (mtp) cc_final: 0.8842 (mtp) REVERT: D 483 GLU cc_start: 0.8473 (tp30) cc_final: 0.8257 (tp30) outliers start: 5 outliers final: 0 residues processed: 161 average time/residue: 0.5387 time to fit residues: 90.5230 Evaluate side-chains 95 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.0020 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 34 GLN D 137 ASN D 188 ASN D 378 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.099779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.076486 restraints weight = 11793.967| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.64 r_work: 0.2873 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6671 Z= 0.163 Angle : 0.606 9.309 9069 Z= 0.312 Chirality : 0.043 0.184 947 Planarity : 0.005 0.040 1172 Dihedral : 4.483 20.724 868 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.46 % Allowed : 11.14 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.29), residues: 790 helix: 0.63 (0.25), residues: 410 sheet: 1.17 (0.76), residues: 43 loop : -0.19 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.015 0.001 TYR D 385 PHE 0.013 0.001 PHE D 369 TRP 0.011 0.001 TRP D 163 HIS 0.002 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 6662) covalent geometry : angle 0.60078 / 0.31 ( 9048) SS BOND : bond 0.00524 / 0.28 ( 6) SS BOND : angle 1.28686 / 0.85 ( 12) hydrogen bonds : bond 0.04775 / 3.26 ( 309) hydrogen bonds : angle 4.84001 / 3.45 ( 951) link_NAG-ASN : bond 0.00367 / 0.20 ( 3) link_NAG-ASN : angle 2.19478 / 1.36 ( 9) *********************** 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 122 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8979 (ptm160) cc_final: 0.8766 (ptm-80) REVERT: A 405 ASN cc_start: 0.8583 (m-40) cc_final: 0.8245 (m110) REVERT: D 145 GLU cc_start: 0.8385 (tp30) cc_final: 0.7864 (tm-30) REVERT: D 163 TRP cc_start: 0.8466 (t60) cc_final: 0.8242 (t60) REVERT: D 190 MET cc_start: 0.9005 (tmm) cc_final: 0.8742 (tmm) REVERT: D 341 LYS cc_start: 0.8625 (mmmm) cc_final: 0.8406 (mppt) REVERT: D 347 THR cc_start: 0.8731 (m) cc_final: 0.8388 (p) REVERT: D 383 MET cc_start: 0.9263 (mtp) cc_final: 0.9023 (mtp) REVERT: D 483 GLU cc_start: 0.8981 (tp30) cc_final: 0.8613 (tp30) REVERT: D 597 GLU cc_start: 0.8705 (tp30) cc_final: 0.8366 (tt0) outliers start: 17 outliers final: 7 residues processed: 109 average time/residue: 0.5116 time to fit residues: 58.5160 Evaluate side-chains 91 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 0.0570 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.097335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.073843 restraints weight = 11832.908| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.61 r_work: 0.2838 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6671 Z= 0.198 Angle : 0.621 12.400 9069 Z= 0.311 Chirality : 0.045 0.251 947 Planarity : 0.004 0.042 1172 Dihedral : 4.486 21.381 868 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.75 % Allowed : 13.02 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.29), residues: 790 helix: 0.89 (0.25), residues: 410 sheet: 1.12 (0.78), residues: 43 loop : -0.04 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.015 0.001 TYR D 385 PHE 0.013 0.001 PHE D 369 TRP 0.009 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 ( 6662) covalent geometry : angle 0.60118 / 0.31 ( 9048) SS BOND : bond 0.00459 / 0.25 ( 6) SS BOND : angle 1.19449 / 0.77 ( 12) hydrogen bonds : bond 0.04889 / 3.35 ( 309) hydrogen bonds : angle 4.72006 / 3.37 ( 951) link_NAG-ASN : bond 0.00327 / 0.20 ( 3) link_NAG-ASN : angle 4.85885 / 2.64 ( 9) *********************** 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 111 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8554 (m-40) cc_final: 0.8214 (m110) REVERT: D 145 GLU cc_start: 0.8432 (tp30) cc_final: 0.7877 (tm-30) REVERT: D 163 TRP cc_start: 0.8465 (t60) cc_final: 0.8264 (t60) REVERT: D 341 LYS cc_start: 0.8700 (mmmm) cc_final: 0.8490 (mppt) REVERT: D 347 THR cc_start: 0.8779 (m) cc_final: 0.8431 (p) REVERT: D 383 MET cc_start: 0.9303 (mtp) cc_final: 0.9080 (mtp) REVERT: D 477 TRP cc_start: 0.8967 (OUTLIER) cc_final: 0.8731 (t-100) REVERT: D 483 GLU cc_start: 0.8995 (tp30) cc_final: 0.8629 (tp30) REVERT: D 597 GLU cc_start: 0.8844 (tp30) cc_final: 0.8638 (tp30) outliers start: 19 outliers final: 9 residues processed: 102 average time/residue: 0.4363 time to fit residues: 46.8189 Evaluate side-chains 97 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.097385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.073887 restraints weight = 11863.121| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.59 r_work: 0.2842 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6671 Z= 0.173 Angle : 0.567 8.221 9069 Z= 0.290 Chirality : 0.044 0.159 947 Planarity : 0.004 0.041 1172 Dihedral : 4.370 20.808 868 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.60 % Allowed : 13.75 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.29), residues: 790 helix: 1.08 (0.25), residues: 409 sheet: 1.18 (0.77), residues: 43 loop : 0.00 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 466 TYR 0.014 0.001 TYR D 385 PHE 0.014 0.001 PHE D 315 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 6662) covalent geometry : angle 0.55564 / 0.29 ( 9048) SS BOND : bond 0.00500 / 0.26 ( 6) SS BOND : angle 1.06742 / 0.63 ( 12) hydrogen bonds : bond 0.04641 / 3.20 ( 309) hydrogen bonds : angle 4.64195 / 3.32 ( 951) link_NAG-ASN : bond 0.00548 / 0.35 ( 3) link_NAG-ASN : angle 3.40098 / 1.90 ( 9) *********************** 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 103 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: D 145 GLU cc_start: 0.8467 (tp30) cc_final: 0.7907 (tm-30) REVERT: D 163 TRP cc_start: 0.8439 (t60) cc_final: 0.8238 (t60) REVERT: D 190 MET cc_start: 0.8995 (tmm) cc_final: 0.8707 (tmm) REVERT: D 298 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8216 (mtt) REVERT: D 341 LYS cc_start: 0.8693 (mmmm) cc_final: 0.8477 (mppt) REVERT: D 383 MET cc_start: 0.9318 (mtp) cc_final: 0.9056 (mtp) REVERT: D 483 GLU cc_start: 0.8997 (tp30) cc_final: 0.8588 (tp30) REVERT: D 491 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8534 (pt) REVERT: D 597 GLU cc_start: 0.8806 (tp30) cc_final: 0.8548 (tp30) outliers start: 18 outliers final: 10 residues processed: 92 average time/residue: 0.4994 time to fit residues: 48.3133 Evaluate side-chains 94 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 531 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 48 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 0.0000 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.095279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.070911 restraints weight = 11184.707| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.60 r_work: 0.2768 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6671 Z= 0.145 Angle : 0.553 7.210 9069 Z= 0.284 Chirality : 0.043 0.171 947 Planarity : 0.004 0.043 1172 Dihedral : 4.242 19.066 868 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.04 % Allowed : 14.04 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.30), residues: 790 helix: 1.20 (0.26), residues: 409 sheet: 1.18 (0.78), residues: 43 loop : 0.02 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 466 TYR 0.013 0.001 TYR D 385 PHE 0.013 0.001 PHE D 369 TRP 0.011 0.001 TRP D 594 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 6662) covalent geometry : angle 0.54563 / 0.28 ( 9048) SS BOND : bond 0.00449 / 0.24 ( 6) SS BOND : angle 1.08669 / 0.67 ( 12) hydrogen bonds : bond 0.04416 / 3.05 ( 309) hydrogen bonds : angle 4.57710 / 3.28 ( 951) link_NAG-ASN : bond 0.00513 / 0.33 ( 3) link_NAG-ASN : angle 2.63862 / 1.53 ( 9) *********************** 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 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: D 114 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8294 (mmmm) REVERT: D 145 GLU cc_start: 0.8474 (tp30) cc_final: 0.7903 (tm-30) REVERT: D 298 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8280 (mtt) REVERT: D 341 LYS cc_start: 0.8697 (mmmm) cc_final: 0.8472 (mppt) REVERT: D 360 MET cc_start: 0.9016 (ttm) cc_final: 0.8801 (ptm) REVERT: D 383 MET cc_start: 0.9305 (mtp) cc_final: 0.9062 (mtp) REVERT: D 483 GLU cc_start: 0.9025 (tp30) cc_final: 0.8628 (tp30) REVERT: D 491 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8555 (pt) REVERT: D 597 GLU cc_start: 0.8774 (tp30) cc_final: 0.8488 (tp30) outliers start: 21 outliers final: 11 residues processed: 91 average time/residue: 0.4932 time to fit residues: 47.0433 Evaluate side-chains 93 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 531 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.098360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.075020 restraints weight = 11914.293| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.61 r_work: 0.2856 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6671 Z= 0.143 Angle : 0.550 7.877 9069 Z= 0.282 Chirality : 0.043 0.188 947 Planarity : 0.004 0.042 1172 Dihedral : 4.152 18.938 868 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.17 % Allowed : 15.20 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.30), residues: 790 helix: 1.30 (0.26), residues: 409 sheet: 1.24 (0.78), residues: 43 loop : 0.10 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.012 0.001 TYR D 385 PHE 0.018 0.001 PHE D 603 TRP 0.009 0.001 TRP D 594 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 6662) covalent geometry : angle 0.54364 / 0.28 ( 9048) SS BOND : bond 0.00446 / 0.24 ( 6) SS BOND : angle 1.13954 / 0.70 ( 12) hydrogen bonds : bond 0.04324 / 2.99 ( 309) hydrogen bonds : angle 4.55166 / 3.26 ( 951) link_NAG-ASN : bond 0.00534 / 0.35 ( 3) link_NAG-ASN : angle 2.47286 / 1.44 ( 9) *********************** 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 95 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 87 GLU cc_start: 0.8008 (pm20) cc_final: 0.7787 (pm20) REVERT: D 114 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8313 (mmmm) REVERT: D 145 GLU cc_start: 0.8452 (tp30) cc_final: 0.7889 (tm-30) REVERT: D 190 MET cc_start: 0.9005 (tmm) cc_final: 0.8769 (tmm) REVERT: D 298 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8402 (mtt) REVERT: D 341 LYS cc_start: 0.8692 (mmmm) cc_final: 0.8487 (mppt) REVERT: D 360 MET cc_start: 0.8979 (ttm) cc_final: 0.8749 (ptm) REVERT: D 383 MET cc_start: 0.9310 (mtp) cc_final: 0.9088 (mtp) REVERT: D 483 GLU cc_start: 0.9012 (tp30) cc_final: 0.8650 (tp30) REVERT: D 491 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8574 (pt) REVERT: D 597 GLU cc_start: 0.8863 (tp30) cc_final: 0.8544 (tp30) REVERT: D 600 ARG cc_start: 0.8356 (ptp90) cc_final: 0.8095 (ptp-110) outliers start: 15 outliers final: 10 residues processed: 87 average time/residue: 0.5450 time to fit residues: 49.8772 Evaluate side-chains 92 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.096976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.073454 restraints weight = 11764.408| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.61 r_work: 0.2830 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6671 Z= 0.179 Angle : 0.574 8.178 9069 Z= 0.295 Chirality : 0.044 0.173 947 Planarity : 0.004 0.040 1172 Dihedral : 4.234 20.203 868 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.60 % Allowed : 14.62 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.30), residues: 790 helix: 1.26 (0.26), residues: 409 sheet: 1.21 (0.78), residues: 43 loop : 0.03 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 357 TYR 0.014 0.001 TYR D 385 PHE 0.017 0.001 PHE D 603 TRP 0.015 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 6662) covalent geometry : angle 0.56813 / 0.29 ( 9048) SS BOND : bond 0.00476 / 0.26 ( 6) SS BOND : angle 1.15459 / 0.70 ( 12) hydrogen bonds : bond 0.04620 / 3.19 ( 309) hydrogen bonds : angle 4.60944 / 3.31 ( 951) link_NAG-ASN : bond 0.00571 / 0.38 ( 3) link_NAG-ASN : angle 2.49444 / 1.44 ( 9) *********************** 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 99 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 403 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8644 (ptm160) REVERT: D 86 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8616 (mp10) REVERT: D 87 GLU cc_start: 0.8088 (pm20) cc_final: 0.7816 (pm20) REVERT: D 114 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8312 (mmmm) REVERT: D 145 GLU cc_start: 0.8435 (tp30) cc_final: 0.7882 (tm-30) REVERT: D 190 MET cc_start: 0.8999 (tmm) cc_final: 0.8709 (tmm) REVERT: D 298 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8506 (mtt) REVERT: D 383 MET cc_start: 0.9318 (mtp) cc_final: 0.9092 (mtp) REVERT: D 483 GLU cc_start: 0.9042 (tp30) cc_final: 0.8644 (tp30) REVERT: D 491 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8521 (pt) REVERT: D 597 GLU cc_start: 0.8811 (tp30) cc_final: 0.8528 (tp30) outliers start: 18 outliers final: 9 residues processed: 89 average time/residue: 0.5869 time to fit residues: 54.6930 Evaluate side-chains 89 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 43 optimal weight: 0.0060 chunk 70 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.095443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.070929 restraints weight = 11092.082| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.59 r_work: 0.2745 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6671 Z= 0.146 Angle : 0.564 8.617 9069 Z= 0.288 Chirality : 0.043 0.183 947 Planarity : 0.004 0.060 1172 Dihedral : 4.148 19.399 868 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.17 % Allowed : 15.48 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.30), residues: 790 helix: 1.41 (0.26), residues: 403 sheet: 0.98 (0.79), residues: 44 loop : 0.08 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 600 TYR 0.012 0.001 TYR D 385 PHE 0.018 0.001 PHE D 603 TRP 0.019 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 6662) covalent geometry : angle 0.55838 / 0.29 ( 9048) SS BOND : bond 0.00449 / 0.24 ( 6) SS BOND : angle 1.20966 / 0.74 ( 12) hydrogen bonds : bond 0.04314 / 2.99 ( 309) hydrogen bonds : angle 4.54474 / 3.26 ( 951) link_NAG-ASN : bond 0.00492 / 0.32 ( 3) link_NAG-ASN : angle 2.34086 / 1.38 ( 9) *********************** 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 92 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8618 (mp10) REVERT: D 87 GLU cc_start: 0.8086 (pm20) cc_final: 0.7782 (pm20) REVERT: D 114 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8286 (mmmm) REVERT: D 145 GLU cc_start: 0.8381 (tp30) cc_final: 0.7856 (tm-30) REVERT: D 163 TRP cc_start: 0.8158 (t60) cc_final: 0.7926 (t60) REVERT: D 190 MET cc_start: 0.8997 (tmm) cc_final: 0.8703 (tmm) REVERT: D 383 MET cc_start: 0.9289 (mtp) cc_final: 0.9072 (mtp) REVERT: D 483 GLU cc_start: 0.9080 (tp30) cc_final: 0.8740 (tp30) REVERT: D 491 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8544 (pt) REVERT: D 597 GLU cc_start: 0.8757 (tp30) cc_final: 0.8486 (tp30) outliers start: 15 outliers final: 11 residues processed: 85 average time/residue: 0.5725 time to fit residues: 51.1525 Evaluate side-chains 90 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 71 optimal weight: 0.0470 chunk 72 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.098367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.075100 restraints weight = 11903.558| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.64 r_work: 0.2842 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6671 Z= 0.138 Angle : 0.558 9.019 9069 Z= 0.285 Chirality : 0.043 0.185 947 Planarity : 0.004 0.040 1172 Dihedral : 4.104 18.552 868 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.03 % Allowed : 15.34 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.30), residues: 790 helix: 1.45 (0.26), residues: 403 sheet: 1.05 (0.77), residues: 44 loop : 0.10 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.012 0.001 TYR D 385 PHE 0.017 0.001 PHE D 603 TRP 0.017 0.001 TRP D 163 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 6662) covalent geometry : angle 0.55281 / 0.28 ( 9048) SS BOND : bond 0.00487 / 0.26 ( 6) SS BOND : angle 1.20008 / 0.74 ( 12) hydrogen bonds : bond 0.04263 / 2.95 ( 309) hydrogen bonds : angle 4.52647 / 3.25 ( 951) link_NAG-ASN : bond 0.00489 / 0.32 ( 3) link_NAG-ASN : angle 2.27077 / 1.33 ( 9) *********************** 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 91 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8554 (ptm160) REVERT: D 87 GLU cc_start: 0.8053 (pm20) cc_final: 0.7750 (pm20) REVERT: D 114 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8322 (mmmm) REVERT: D 145 GLU cc_start: 0.8370 (tp30) cc_final: 0.7845 (tm-30) REVERT: D 383 MET cc_start: 0.9293 (mtp) cc_final: 0.9079 (mtp) REVERT: D 483 GLU cc_start: 0.9049 (tp30) cc_final: 0.8698 (tp30) REVERT: D 491 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8555 (pt) REVERT: D 597 GLU cc_start: 0.8850 (tp30) cc_final: 0.8607 (tp30) outliers start: 14 outliers final: 11 residues processed: 85 average time/residue: 0.6072 time to fit residues: 54.2713 Evaluate side-chains 91 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 44 optimal weight: 0.3980 chunk 52 optimal weight: 0.0270 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.096406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.071740 restraints weight = 10999.635| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.61 r_work: 0.2758 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6671 Z= 0.137 Angle : 0.566 9.253 9069 Z= 0.287 Chirality : 0.043 0.187 947 Planarity : 0.004 0.062 1172 Dihedral : 4.079 18.117 868 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.03 % Allowed : 15.63 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.30), residues: 790 helix: 1.47 (0.26), residues: 403 sheet: 1.08 (0.78), residues: 44 loop : 0.12 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 600 TYR 0.012 0.001 TYR D 385 PHE 0.017 0.001 PHE D 603 TRP 0.021 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6662) covalent geometry : angle 0.56025 / 0.29 ( 9048) SS BOND : bond 0.00498 / 0.26 ( 6) SS BOND : angle 1.20139 / 0.74 ( 12) hydrogen bonds : bond 0.04210 / 2.92 ( 309) hydrogen bonds : angle 4.49434 / 3.22 ( 951) link_NAG-ASN : bond 0.00485 / 0.32 ( 3) link_NAG-ASN : angle 2.23658 / 1.32 ( 9) ********************** 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 94 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8534 (ptm160) REVERT: D 87 GLU cc_start: 0.8064 (pm20) cc_final: 0.7732 (pm20) REVERT: D 114 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8295 (mmmm) REVERT: D 145 GLU cc_start: 0.8391 (tp30) cc_final: 0.7855 (tm-30) REVERT: D 190 MET cc_start: 0.8954 (tmm) cc_final: 0.8713 (tmm) REVERT: D 383 MET cc_start: 0.9287 (mtp) cc_final: 0.9075 (mtp) REVERT: D 483 GLU cc_start: 0.9087 (tp30) cc_final: 0.8745 (tp30) REVERT: D 597 GLU cc_start: 0.8717 (tp30) cc_final: 0.8516 (tp30) outliers start: 14 outliers final: 11 residues processed: 88 average time/residue: 0.5980 time to fit residues: 55.3667 Evaluate side-chains 93 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.097693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.074579 restraints weight = 11842.268| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.63 r_work: 0.2847 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6671 Z= 0.167 Angle : 0.584 9.191 9069 Z= 0.298 Chirality : 0.044 0.182 947 Planarity : 0.004 0.040 1172 Dihedral : 4.125 19.074 868 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.74 % Allowed : 16.35 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.30), residues: 790 helix: 1.45 (0.26), residues: 403 sheet: 1.11 (0.78), residues: 44 loop : 0.11 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 357 TYR 0.013 0.001 TYR D 385 PHE 0.017 0.001 PHE D 603 TRP 0.021 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 6662) covalent geometry : angle 0.57882 / 0.30 ( 9048) SS BOND : bond 0.00469 / 0.25 ( 6) SS BOND : angle 1.19612 / 0.73 ( 12) hydrogen bonds : bond 0.04369 / 3.02 ( 309) hydrogen bonds : angle 4.52513 / 3.25 ( 951) link_NAG-ASN : bond 0.00443 / 0.29 ( 3) link_NAG-ASN : angle 2.32603 / 1.35 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2440.67 seconds wall clock time: 42 minutes 19.08 seconds (2539.08 seconds total)