Starting phenix.real_space_refine on Thu Jul 2 04:14:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dma_27532/07_2026/8dma_27532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dma_27532/07_2026/8dma_27532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dma_27532/07_2026/8dma_27532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dma_27532/07_2026/8dma_27532.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dma_27532/07_2026/8dma_27532.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dma_27532/07_2026/8dma_27532.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dma_27532/07_2026/8dma_27532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dma_27532/07_2026/8dma_27532.map" } resolution = 2.79 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 4142 2.51 5 N 1089 2.21 5 O 1219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 6487 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 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: 1.22, per 1000 atoms: 0.19 Number of scatterers: 6487 At special positions: 0 Unit cell: (77, 87, 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 1219 8.00 N 1089 7.00 C 4142 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=2.03 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 525 " distance=2.04 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=2.02 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: 0.43 Conformation dependent library (CDL) restraints added in 294.0 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: 1502 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 56.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.781A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.564A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.301A pdb=" N ARG A 408 " --> pdb=" O ASP 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: 4.051A pdb=" N GLN D 34 " --> pdb=" O ASN D 30 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.547A pdb=" N THR D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) 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: 3.749A pdb=" N GLU D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.512A 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: 3.700A pdb=" N SER D 106 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.819A 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: 5.092A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.706A 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 218 through 252 removed outlier: 3.658A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.622A 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: 3.557A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.709A 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: 3.868A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.565A 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: 3.615A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.449A 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: 3.605A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.743A 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: 4.242A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.687A 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: 4.159A 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 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 Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 133 removed outlier: 3.539A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.993A 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 352 removed outlier: 6.273A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 882 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: 0.81 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2077 1.34 - 1.47: 1743 1.47 - 1.59: 2791 1.59 - 1.71: 0 1.71 - 1.84: 58 Bond restraints: 6669 Sorted by residual: 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 5.20e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.58e+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 3.70e+00 bond pdb=" CG LEU D 558 " pdb=" CD1 LEU D 558 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.42e+00 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 6664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 8675 1.82 - 3.63: 315 3.63 - 5.45: 42 5.45 - 7.27: 19 7.27 - 9.08: 7 Bond angle restraints: 9058 Sorted by residual: angle pdb=" C SER A 359 " pdb=" N ASN A 360 " pdb=" CA ASN A 360 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C VAL D 364 " pdb=" CA VAL D 364 " pdb=" CB VAL D 364 " ideal model delta sigma weight residual 113.22 116.94 -3.72 1.12e+00 7.97e-01 1.10e+01 angle pdb=" CA VAL D 364 " pdb=" CB VAL D 364 " pdb=" CG1 VAL D 364 " ideal model delta sigma weight residual 110.40 115.87 -5.47 1.70e+00 3.46e-01 1.03e+01 angle pdb=" N ALA A 372 " pdb=" CA ALA A 372 " pdb=" C ALA A 372 " ideal model delta sigma weight residual 109.81 116.76 -6.95 2.21e+00 2.05e-01 9.89e+00 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 121.44 -7.04 2.30e+00 1.89e-01 9.38e+00 ... (remaining 9053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 3541 17.14 - 34.28: 330 34.28 - 51.42: 46 51.42 - 68.56: 6 68.56 - 85.70: 8 Dihedral angle restraints: 3931 sinusoidal: 1594 harmonic: 2337 Sorted by residual: 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 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ALA D 396 " pdb=" C ALA D 396 " pdb=" N ASN D 397 " pdb=" CA ASN D 397 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA THR D 445 " pdb=" C THR D 445 " pdb=" N ILE D 446 " pdb=" CA ILE D 446 " ideal model delta harmonic sigma weight residual 180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 3928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 619 0.046 - 0.092: 234 0.092 - 0.138: 81 0.138 - 0.184: 14 0.184 - 0.230: 3 Chirality restraints: 951 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 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA GLU D 182 " pdb=" N GLU D 182 " pdb=" C GLU D 182 " pdb=" CB GLU D 182 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU D 558 " pdb=" CB LEU D 558 " pdb=" CD1 LEU D 558 " pdb=" CD2 LEU D 558 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 948 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " -0.045 5.00e-02 4.00e+02 6.69e-02 7.17e+00 pdb=" N PRO A 373 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 224 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.11e+00 pdb=" C GLU D 224 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU D 224 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP D 225 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 468 " 0.040 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO D 469 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 469 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 469 " 0.034 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1333 2.78 - 3.31: 5871 3.31 - 3.84: 11379 3.84 - 4.37: 13370 4.37 - 4.90: 22664 Nonbonded interactions: 54617 Sorted by model distance: nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.244 3.040 nonbonded pdb=" O ILE D 151 " pdb=" OG SER D 155 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR A 500 " pdb=" OH TYR D 41 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.340 3.040 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.350 3.120 ... (remaining 54612 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: 4.170 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.720 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:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 : 0.005 0.064 6678 Z= 0.236 Angle : 0.841 9.082 9079 Z= 0.442 Chirality : 0.055 0.230 951 Planarity : 0.007 0.067 1172 Dihedral : 13.322 85.700 2411 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.14 % Allowed : 0.29 % Favored : 99.57 % 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: -1.53 (0.26), residues: 790 helix: -1.27 (0.22), residues: 399 sheet: 0.24 (0.64), residues: 60 loop : -0.69 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 403 TYR 0.029 0.002 TYR D 385 PHE 0.021 0.002 PHE D 369 TRP 0.025 0.002 TRP D 163 HIS 0.005 0.002 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 ( 6669) covalent geometry : angle 0.83298 / 0.44 ( 9058) SS BOND : bond 0.00608 / 0.35 ( 6) SS BOND : angle 1.57620 / 1.00 ( 12) hydrogen bonds : bond 0.13661 / 9.15 ( 307) hydrogen bonds : angle 6.78139 / 4.58 ( 882) link_NAG-ASN : bond 0.00646 / 0.36 ( 3) link_NAG-ASN : angle 3.32018 / 1.84 ( 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 109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.254 Fit side-chains REVERT: A 386 LYS cc_start: 0.9051 (mttt) cc_final: 0.8823 (mptt) REVERT: A 420 ASP cc_start: 0.8793 (m-30) cc_final: 0.8478 (m-30) REVERT: D 564 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8453 (mm-30) REVERT: D 597 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8133 (tm-30) REVERT: D 607 ASN cc_start: 0.8700 (t0) cc_final: 0.8418 (t0) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.6284 time to fit residues: 71.5789 Evaluate side-chains 68 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 188 ASN D 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.091276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.070686 restraints weight = 13236.120| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.89 r_work: 0.2841 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6678 Z= 0.157 Angle : 0.571 6.045 9079 Z= 0.292 Chirality : 0.043 0.175 951 Planarity : 0.005 0.046 1172 Dihedral : 4.703 19.333 869 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.30 % Allowed : 8.50 % Favored : 90.20 % 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: -0.05 (0.29), residues: 790 helix: 0.24 (0.25), residues: 395 sheet: 0.14 (0.65), residues: 59 loop : -0.22 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 600 TYR 0.013 0.001 TYR D 385 PHE 0.018 0.001 PHE D 369 TRP 0.018 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 6669) covalent geometry : angle 0.56568 / 0.29 ( 9058) SS BOND : bond 0.00478 / 0.30 ( 6) SS BOND : angle 1.13269 / 0.74 ( 12) hydrogen bonds : bond 0.04267 / 2.78 ( 307) hydrogen bonds : angle 4.88794 / 3.33 ( 882) link_NAG-ASN : bond 0.00434 / 0.29 ( 3) link_NAG-ASN : angle 2.28627 / 1.57 ( 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 84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.279 Fit side-chains REVERT: D 23 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8252 (mp0) REVERT: D 149 ASP cc_start: 0.8504 (m-30) cc_final: 0.8283 (p0) REVERT: D 163 TRP cc_start: 0.8455 (t60) cc_final: 0.8132 (t60) REVERT: D 597 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8302 (tm-30) REVERT: D 607 ASN cc_start: 0.8855 (t0) cc_final: 0.8411 (t0) outliers start: 9 outliers final: 3 residues processed: 79 average time/residue: 0.5314 time to fit residues: 44.2440 Evaluate side-chains 72 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 390 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.087831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.067268 restraints weight = 13340.568| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.85 r_work: 0.2765 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 6678 Z= 0.264 Angle : 0.625 7.226 9079 Z= 0.321 Chirality : 0.047 0.194 951 Planarity : 0.004 0.039 1172 Dihedral : 4.806 19.833 869 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.45 % Allowed : 11.24 % Favored : 86.31 % 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: 0.34 (0.29), residues: 790 helix: 0.58 (0.26), residues: 396 sheet: 0.04 (0.65), residues: 59 loop : 0.02 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 600 TYR 0.017 0.002 TYR D 385 PHE 0.018 0.001 PHE D 369 TRP 0.014 0.001 TRP D 163 HIS 0.006 0.002 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.26 ( 6669) covalent geometry : angle 0.61923 / 0.32 ( 9058) SS BOND : bond 0.00540 / 0.37 ( 6) SS BOND : angle 1.19000 / 0.70 ( 12) hydrogen bonds : bond 0.04839 / 3.12 ( 307) hydrogen bonds : angle 4.78804 / 3.25 ( 882) link_NAG-ASN : bond 0.00412 / 0.27 ( 3) link_NAG-ASN : angle 2.54914 / 1.76 ( 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 85 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.215 Fit side-chains REVERT: A 385 THR cc_start: 0.9437 (p) cc_final: 0.9236 (p) REVERT: A 386 LYS cc_start: 0.9332 (mttt) cc_final: 0.8892 (mptt) REVERT: A 496 SER cc_start: 0.8360 (p) cc_final: 0.8072 (m) REVERT: D 149 ASP cc_start: 0.8611 (m-30) cc_final: 0.8409 (p0) REVERT: D 471 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8224 (pm20) REVERT: D 579 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8457 (ttm) REVERT: D 597 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8385 (tm-30) REVERT: D 607 ASN cc_start: 0.8844 (t0) cc_final: 0.8370 (t0) outliers start: 17 outliers final: 4 residues processed: 80 average time/residue: 0.5344 time to fit residues: 44.8310 Evaluate side-chains 73 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 2 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 378 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.089991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.069834 restraints weight = 13394.015| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.85 r_work: 0.2822 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6678 Z= 0.140 Angle : 0.557 7.519 9079 Z= 0.282 Chirality : 0.043 0.161 951 Planarity : 0.004 0.035 1172 Dihedral : 4.462 17.802 869 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.30 % Allowed : 12.54 % Favored : 86.17 % 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 (0.30), residues: 790 helix: 0.92 (0.26), residues: 389 sheet: 0.06 (0.66), residues: 59 loop : 0.16 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 600 TYR 0.012 0.001 TYR D 385 PHE 0.016 0.001 PHE D 369 TRP 0.010 0.001 TRP D 163 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 6669) covalent geometry : angle 0.55256 / 0.28 ( 9058) SS BOND : bond 0.00441 / 0.28 ( 6) SS BOND : angle 0.94930 / 0.60 ( 12) hydrogen bonds : bond 0.04008 / 2.61 ( 307) hydrogen bonds : angle 4.58046 / 3.11 ( 882) link_NAG-ASN : bond 0.00366 / 0.23 ( 3) link_NAG-ASN : angle 2.22143 / 1.57 ( 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 85 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.260 Fit side-chains REVERT: A 385 THR cc_start: 0.9425 (p) cc_final: 0.9220 (p) REVERT: A 386 LYS cc_start: 0.9349 (mttt) cc_final: 0.8886 (mptt) REVERT: D 182 GLU cc_start: 0.8927 (pt0) cc_final: 0.8461 (pp20) REVERT: D 471 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: D 472 GLN cc_start: 0.8124 (mp10) cc_final: 0.7671 (mp10) REVERT: D 597 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8443 (tm-30) REVERT: D 607 ASN cc_start: 0.8810 (t0) cc_final: 0.8368 (t0) outliers start: 9 outliers final: 6 residues processed: 83 average time/residue: 0.5673 time to fit residues: 49.3808 Evaluate side-chains 75 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 390 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 556 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.088258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.067983 restraints weight = 13442.514| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.85 r_work: 0.2789 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6678 Z= 0.209 Angle : 0.590 7.698 9079 Z= 0.300 Chirality : 0.045 0.208 951 Planarity : 0.004 0.044 1172 Dihedral : 4.519 19.289 869 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.16 % Allowed : 13.26 % Favored : 84.58 % 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: 0.78 (0.30), residues: 790 helix: 0.98 (0.26), residues: 389 sheet: 0.01 (0.64), residues: 59 loop : 0.23 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 600 TYR 0.016 0.001 TYR D 381 PHE 0.018 0.001 PHE D 369 TRP 0.009 0.001 TRP D 163 HIS 0.005 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 ( 6669) covalent geometry : angle 0.58475 / 0.30 ( 9058) SS BOND : bond 0.00514 / 0.35 ( 6) SS BOND : angle 0.99919 / 0.60 ( 12) hydrogen bonds : bond 0.04395 / 2.84 ( 307) hydrogen bonds : angle 4.60985 / 3.14 ( 882) link_NAG-ASN : bond 0.00331 / 0.22 ( 3) link_NAG-ASN : angle 2.36369 / 1.63 ( 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 80 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.243 Fit side-chains REVERT: A 386 LYS cc_start: 0.9353 (mttt) cc_final: 0.8984 (mtmm) REVERT: A 493 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8110 (mmm160) REVERT: D 182 GLU cc_start: 0.8945 (pt0) cc_final: 0.8476 (pp20) REVERT: D 471 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8242 (pm20) REVERT: D 472 GLN cc_start: 0.8247 (mp10) cc_final: 0.7965 (mp10) REVERT: D 597 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8471 (tm-30) REVERT: D 607 ASN cc_start: 0.8761 (t0) cc_final: 0.8283 (t0) outliers start: 15 outliers final: 7 residues processed: 75 average time/residue: 0.6369 time to fit residues: 49.9553 Evaluate side-chains 72 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** 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 = 0.3287 r_free = 0.3287 target = 0.089112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.068893 restraints weight = 13417.359| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.86 r_work: 0.2806 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6678 Z= 0.165 Angle : 0.568 7.922 9079 Z= 0.287 Chirality : 0.044 0.214 951 Planarity : 0.004 0.044 1172 Dihedral : 4.396 18.763 869 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.02 % Allowed : 14.12 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.94 (0.30), residues: 790 helix: 1.12 (0.26), residues: 390 sheet: -0.06 (0.63), residues: 59 loop : 0.33 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 600 TYR 0.013 0.001 TYR D 381 PHE 0.016 0.001 PHE D 369 TRP 0.009 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 6669) covalent geometry : angle 0.56287 / 0.29 ( 9058) SS BOND : bond 0.00474 / 0.30 ( 6) SS BOND : angle 0.92336 / 0.59 ( 12) hydrogen bonds : bond 0.04106 / 2.66 ( 307) hydrogen bonds : angle 4.52583 / 3.08 ( 882) link_NAG-ASN : bond 0.00321 / 0.20 ( 3) link_NAG-ASN : angle 2.30537 / 1.60 ( 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 78 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.9397 (mttt) cc_final: 0.9008 (mtmm) REVERT: A 493 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8116 (mmm160) REVERT: D 182 GLU cc_start: 0.8918 (pt0) cc_final: 0.8439 (pp20) REVERT: D 471 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: D 472 GLN cc_start: 0.8212 (mp10) cc_final: 0.7845 (mp10) REVERT: D 579 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8546 (ttm) REVERT: D 597 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8466 (tm-30) REVERT: D 607 ASN cc_start: 0.8732 (t0) cc_final: 0.8092 (t0) outliers start: 14 outliers final: 8 residues processed: 75 average time/residue: 0.6692 time to fit residues: 52.4334 Evaluate side-chains 71 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** 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 = 0.3292 r_free = 0.3292 target = 0.089399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.069422 restraints weight = 13337.762| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.84 r_work: 0.2811 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6678 Z= 0.152 Angle : 0.564 8.191 9079 Z= 0.284 Chirality : 0.043 0.214 951 Planarity : 0.004 0.051 1172 Dihedral : 4.334 18.966 869 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.16 % Allowed : 14.84 % Favored : 83.00 % 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: 1.00 (0.30), residues: 790 helix: 1.18 (0.26), residues: 390 sheet: -0.10 (0.63), residues: 59 loop : 0.37 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 600 TYR 0.013 0.001 TYR D 385 PHE 0.016 0.001 PHE D 369 TRP 0.008 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 6669) covalent geometry : angle 0.55977 / 0.28 ( 9058) SS BOND : bond 0.00465 / 0.29 ( 6) SS BOND : angle 0.84149 / 0.52 ( 12) hydrogen bonds : bond 0.04025 / 2.61 ( 307) hydrogen bonds : angle 4.50041 / 3.07 ( 882) link_NAG-ASN : bond 0.00296 / 0.19 ( 3) link_NAG-ASN : angle 2.21607 / 1.51 ( 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 75 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.9381 (mttt) cc_final: 0.9055 (mmmm) REVERT: D 171 GLU cc_start: 0.7925 (mp0) cc_final: 0.7617 (mp0) REVERT: D 182 GLU cc_start: 0.8890 (pt0) cc_final: 0.8405 (pp20) REVERT: D 471 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8149 (pm20) REVERT: D 472 GLN cc_start: 0.8222 (mp10) cc_final: 0.7935 (mp10) REVERT: D 579 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8520 (ttm) REVERT: D 597 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8452 (tm-30) REVERT: D 607 ASN cc_start: 0.8658 (t0) cc_final: 0.8181 (t0) outliers start: 15 outliers final: 9 residues processed: 73 average time/residue: 0.6077 time to fit residues: 46.4232 Evaluate side-chains 70 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 39 optimal weight: 0.0870 chunk 42 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** 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 = 0.3296 r_free = 0.3296 target = 0.089759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.069739 restraints weight = 13259.302| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.83 r_work: 0.2813 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6678 Z= 0.147 Angle : 0.566 8.747 9079 Z= 0.284 Chirality : 0.043 0.218 951 Planarity : 0.004 0.058 1172 Dihedral : 4.297 18.962 869 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.87 % Allowed : 14.99 % Favored : 83.14 % 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: 1.06 (0.30), residues: 790 helix: 1.25 (0.26), residues: 390 sheet: -0.13 (0.63), residues: 59 loop : 0.39 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 600 TYR 0.013 0.001 TYR D 385 PHE 0.016 0.001 PHE D 369 TRP 0.008 0.001 TRP D 594 HIS 0.004 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 6669) covalent geometry : angle 0.56207 / 0.28 ( 9058) SS BOND : bond 0.00443 / 0.28 ( 6) SS BOND : angle 0.81872 / 0.51 ( 12) hydrogen bonds : bond 0.03973 / 2.58 ( 307) hydrogen bonds : angle 4.47990 / 3.06 ( 882) link_NAG-ASN : bond 0.00299 / 0.19 ( 3) link_NAG-ASN : angle 2.20909 / 1.52 ( 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 74 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.9372 (mttt) cc_final: 0.9092 (mmmm) REVERT: A 493 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8214 (mmm160) REVERT: D 171 GLU cc_start: 0.8007 (mp0) cc_final: 0.7592 (mp0) REVERT: D 182 GLU cc_start: 0.8880 (pt0) cc_final: 0.8427 (pp20) REVERT: D 471 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8157 (pm20) REVERT: D 472 GLN cc_start: 0.8239 (mp10) cc_final: 0.8017 (mp10) REVERT: D 579 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8574 (ttm) REVERT: D 597 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8537 (tm-30) REVERT: D 607 ASN cc_start: 0.8680 (t0) cc_final: 0.8309 (t0) outliers start: 13 outliers final: 8 residues processed: 71 average time/residue: 0.5985 time to fit residues: 44.5645 Evaluate side-chains 71 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 59 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 30 optimal weight: 0.0470 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 71 optimal weight: 0.2980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** 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 = 0.3312 r_free = 0.3312 target = 0.090439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.070310 restraints weight = 13388.381| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.87 r_work: 0.2826 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6678 Z= 0.126 Angle : 0.559 9.019 9079 Z= 0.280 Chirality : 0.042 0.215 951 Planarity : 0.004 0.060 1172 Dihedral : 4.286 18.596 869 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.16 % Allowed : 14.84 % Favored : 83.00 % 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: 1.29 (0.26), residues: 391 sheet: -0.11 (0.63), residues: 59 loop : 0.42 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 600 TYR 0.012 0.001 TYR D 385 PHE 0.015 0.001 PHE D 369 TRP 0.008 0.001 TRP D 163 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 6669) covalent geometry : angle 0.55443 / 0.28 ( 9058) SS BOND : bond 0.00537 / 0.30 ( 6) SS BOND : angle 1.20001 / 0.72 ( 12) hydrogen bonds : bond 0.03813 / 2.48 ( 307) hydrogen bonds : angle 4.46429 / 3.04 ( 882) link_NAG-ASN : bond 0.00288 / 0.18 ( 3) link_NAG-ASN : angle 2.11068 / 1.44 ( 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 78 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.9389 (mttt) cc_final: 0.8897 (mptt) REVERT: A 493 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8172 (mmm160) REVERT: D 171 GLU cc_start: 0.7932 (mp0) cc_final: 0.7472 (mp0) REVERT: D 182 GLU cc_start: 0.8846 (pt0) cc_final: 0.8383 (pp20) REVERT: D 471 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: D 472 GLN cc_start: 0.8241 (mp10) cc_final: 0.7980 (mp10) REVERT: D 597 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8528 (tm-30) REVERT: D 607 ASN cc_start: 0.8661 (t0) cc_final: 0.8270 (t0) outliers start: 15 outliers final: 8 residues processed: 75 average time/residue: 0.6051 time to fit residues: 47.5831 Evaluate side-chains 72 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS 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 42 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** 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 = 0.3299 r_free = 0.3299 target = 0.089662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.069541 restraints weight = 13239.135| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.86 r_work: 0.2816 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6678 Z= 0.148 Angle : 0.572 8.971 9079 Z= 0.286 Chirality : 0.043 0.221 951 Planarity : 0.004 0.064 1172 Dihedral : 4.297 18.905 869 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.02 % Allowed : 15.27 % Favored : 82.71 % 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: 1.11 (0.30), residues: 790 helix: 1.30 (0.26), residues: 392 sheet: -0.16 (0.62), residues: 59 loop : 0.40 (0.37), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 600 TYR 0.013 0.001 TYR D 385 PHE 0.016 0.001 PHE D 369 TRP 0.008 0.001 TRP D 594 HIS 0.004 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 6669) covalent geometry : angle 0.56676 / 0.29 ( 9058) SS BOND : bond 0.00474 / 0.29 ( 6) SS BOND : angle 1.20913 / 0.76 ( 12) hydrogen bonds : bond 0.03917 / 2.53 ( 307) hydrogen bonds : angle 4.43733 / 3.03 ( 882) link_NAG-ASN : bond 0.00298 / 0.19 ( 3) link_NAG-ASN : angle 2.16666 / 1.47 ( 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 79 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.9407 (mttt) cc_final: 0.8923 (mptt) REVERT: A 493 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8175 (mmm160) REVERT: D 171 GLU cc_start: 0.7918 (mp0) cc_final: 0.7499 (mp0) REVERT: D 182 GLU cc_start: 0.8845 (pt0) cc_final: 0.8387 (pp20) REVERT: D 471 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8135 (pm20) REVERT: D 472 GLN cc_start: 0.8253 (mp10) cc_final: 0.8049 (mp10) REVERT: D 597 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8538 (tm-30) REVERT: D 607 ASN cc_start: 0.8674 (t0) cc_final: 0.8292 (t0) outliers start: 14 outliers final: 9 residues processed: 75 average time/residue: 0.6222 time to fit residues: 49.0243 Evaluate side-chains 75 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS 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 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 78 optimal weight: 0.0370 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.0770 chunk 8 optimal weight: 0.9980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** 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 = 0.3314 r_free = 0.3314 target = 0.090560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.070479 restraints weight = 13193.322| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.85 r_work: 0.2830 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6678 Z= 0.125 Angle : 0.569 9.138 9079 Z= 0.283 Chirality : 0.042 0.213 951 Planarity : 0.004 0.063 1172 Dihedral : 4.220 18.887 869 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.87 % Allowed : 15.56 % Favored : 82.56 % 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: 1.20 (0.30), residues: 790 helix: 1.40 (0.26), residues: 391 sheet: -0.12 (0.63), residues: 59 loop : 0.41 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 600 TYR 0.011 0.001 TYR D 385 PHE 0.015 0.001 PHE D 369 TRP 0.008 0.001 TRP D 594 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 6669) covalent geometry : angle 0.56504 / 0.28 ( 9058) SS BOND : bond 0.00429 / 0.26 ( 6) SS BOND : angle 1.02480 / 0.65 ( 12) hydrogen bonds : bond 0.03728 / 2.42 ( 307) hydrogen bonds : angle 4.39153 / 3.00 ( 882) link_NAG-ASN : bond 0.00289 / 0.18 ( 3) link_NAG-ASN : angle 2.06648 / 1.39 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1940.29 seconds wall clock time: 33 minutes 57.77 seconds (2037.77 seconds total)