Starting phenix.real_space_refine on Thu Jul 2 04:15:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8aqs_15588/07_2026/8aqs_15588.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aqs_15588/07_2026/8aqs_15588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8aqs_15588/07_2026/8aqs_15588.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8aqs_15588/07_2026/8aqs_15588.cif" model { file = "/net/cci-nas-00/data/ceres_data/8aqs_15588/07_2026/8aqs_15588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aqs_15588/07_2026/8aqs_15588.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8aqs_15588/07_2026/8aqs_15588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aqs_15588/07_2026/8aqs_15588.map" } resolution = 2.92 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= -0.000 sd= 0.030 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4155 2.51 5 N 1073 2.21 5 O 1227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 6493 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "B" Number of atoms: 4864 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Conformer: "C" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} bond proxies already assigned to first conformer: 4985 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: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 72 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.25, per 1000 atoms: 0.35 Number of scatterers: 6493 At special positions: 0 Unit cell: (89.2672, 78.1088, 118.685, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1227 8.00 N 1073 7.00 C 4155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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 B 901 " - " ASN B 53 " " NAG B 902 " - " ASN B 90 " " NAG B 903 " - " ASN B 103 " " NAG B 904 " - " ASN B 546 " " NAG B 905 " - " ASN B 322 " Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 521.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 906 " pdb="ZN ZN B 906 " - pdb=" NE2 HIS B 374 " pdb="ZN ZN B 906 " - pdb=" NE2 HIS B 378 " 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 53.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.105A pdb=" N PHE A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.662A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.902A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 53 removed outlier: 3.945A pdb=" N TYR B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 81 Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 109 through 130 Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 157 through 194 removed outlier: 3.663A pdb=" N ARG B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 169 " --> pdb=" O TRP B 165 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 220 through 252 removed outlier: 4.068A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 232 " --> pdb=" O HIS B 228 " (cutoff:3.500A) Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.739A pdb=" N TYR B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 303 through 311 removed outlier: 3.599A pdb=" N ALA B 311 " --> pdb=" O ILE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 319 removed outlier: 3.505A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 removed outlier: 4.166A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.889A pdb=" N PHE B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 370 " --> pdb=" O MET B 366 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 removed outlier: 3.528A pdb=" N ARG B 393 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 412 removed outlier: 3.664A pdb=" N SER B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 412 " --> pdb=" O MET B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 Processing helix chain 'B' and resid 431 through 444 removed outlier: 3.903A pdb=" N ILE B 436 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 466 Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.654A pdb=" N ARG B 482 " --> pdb=" O TRP B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.590A pdb=" N SER B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 533 removed outlier: 3.645A pdb=" N THR B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.980A pdb=" N GLY B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 574 Processing helix chain 'B' and resid 581 through 599 Proline residue: B 590 - end of helix 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 'B' and resid 262 through 263 removed outlier: 6.112A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 347 through 352 removed outlier: 6.053A pdb=" N ASP B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) 292 hydrogen bonds defined for protein. 818 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: 0.98 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: 1.23 - 1.34: 2074 1.34 - 1.46: 1675 1.46 - 1.58: 2869 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6676 Sorted by residual: bond pdb=" C1 NAG B 902 " pdb=" O5 NAG B 902 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C1 NAG B 904 " pdb=" O5 NAG B 904 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C1 NAG B 903 " pdb=" O5 NAG B 903 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.66e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.40e+00 ... (remaining 6671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 8959 2.07 - 4.13: 102 4.13 - 6.20: 13 6.20 - 8.26: 1 8.26 - 10.33: 1 Bond angle restraints: 9076 Sorted by residual: angle pdb=" C PHE A 371 " pdb=" N ALA A 372 " pdb=" CA ALA A 372 " ideal model delta sigma weight residual 121.80 132.13 -10.33 2.44e+00 1.68e-01 1.79e+01 angle pdb=" C PRO B 84 " pdb=" N LEU B 85 " pdb=" CA LEU B 85 " ideal model delta sigma weight residual 121.54 127.71 -6.17 1.91e+00 2.74e-01 1.04e+01 angle pdb=" N ILE A 418 " pdb=" CA ILE A 418 " pdb=" C ILE A 418 " ideal model delta sigma weight residual 111.81 109.22 2.59 8.60e-01 1.35e+00 9.08e+00 angle pdb=" N LYS B 174 " pdb=" CA LYS B 174 " pdb=" C LYS B 174 " ideal model delta sigma weight residual 112.72 109.37 3.35 1.14e+00 7.69e-01 8.64e+00 angle pdb=" N GLN B 175 " pdb=" CA GLN B 175 " pdb=" C GLN B 175 " ideal model delta sigma weight residual 114.64 110.19 4.45 1.52e+00 4.33e-01 8.55e+00 ... (remaining 9071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 3461 15.84 - 31.67: 327 31.67 - 47.51: 75 47.51 - 63.35: 10 63.35 - 79.18: 9 Dihedral angle restraints: 3882 sinusoidal: 1563 harmonic: 2319 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 93.00 127.82 -34.82 1 1.00e+01 1.00e-02 1.72e+01 dihedral pdb=" CA THR A 500 " pdb=" C THR A 500 " pdb=" N TYR A 501 " pdb=" CA TYR A 501 " ideal model delta harmonic sigma weight residual 180.00 163.37 16.63 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA PRO A 384 " pdb=" C PRO A 384 " pdb=" N THR A 385 " pdb=" CA THR A 385 " ideal model delta harmonic sigma weight residual 180.00 163.89 16.11 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 3879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 897 0.081 - 0.163: 66 0.163 - 0.244: 0 0.244 - 0.325: 0 0.325 - 0.406: 1 Chirality restraints: 964 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CB ILE B 407 " pdb=" CA ILE B 407 " pdb=" CG1 ILE B 407 " pdb=" CG2 ILE B 407 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" C1 NAG B 904 " pdb=" ND2 ASN B 546 " pdb=" C2 NAG B 904 " pdb=" O5 NAG B 904 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 961 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 145 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO B 146 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 234 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO B 235 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 235 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 235 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 293 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.64e+00 pdb=" C VAL B 293 " 0.022 2.00e-02 2.50e+03 pdb=" O VAL B 293 " -0.008 2.00e-02 2.50e+03 pdb=" N THR B 294 " -0.008 2.00e-02 2.50e+03 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 996 2.76 - 3.30: 5887 3.30 - 3.83: 10338 3.83 - 4.37: 12079 4.37 - 4.90: 21510 Nonbonded interactions: 50810 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" O ILE B 358 " model vdw 2.227 3.040 nonbonded pdb=" NE ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.250 3.120 nonbonded pdb=" NH2 ARG A 454 " pdb=" O SER A 469 " model vdw 2.307 3.120 nonbonded pdb=" OG SER A 438 " pdb=" OD2 ASP A 442 " model vdw 2.337 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.369 3.040 ... (remaining 50805 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.430 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.080 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6688 Z= 0.132 Angle : 0.560 10.326 9102 Z= 0.295 Chirality : 0.043 0.406 964 Planarity : 0.004 0.055 1170 Dihedral : 13.389 79.184 2382 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.93 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.71 (0.31), residues: 785 helix: 1.81 (0.29), residues: 357 sheet: 1.33 (0.79), residues: 45 loop : -0.97 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.020 0.001 TYR A 501 PHE 0.018 0.001 PHE B 400 TRP 0.013 0.001 TRP B 477 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 6676) covalent geometry : angle 0.54345 / 0.29 ( 9076) SS BOND : bond 0.00134 / 0.06 ( 4) SS BOND : angle 0.54890 / 0.30 ( 8) hydrogen bonds : bond 0.15023 / 9.97 ( 292) hydrogen bonds : angle 4.79337 / 3.31 ( 818) metal coordination : bond 0.00079 / 0.04 ( 2) link_NAG-ASN : bond 0.00640 / 0.34 ( 6) link_NAG-ASN : angle 3.04197 / 1.98 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.357 Fit side-chains REVERT: A 440 LYS cc_start: 0.8615 (mttm) cc_final: 0.8305 (mmtm) REVERT: A 444 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8226 (mtpm) REVERT: A 467 ASP cc_start: 0.8491 (t0) cc_final: 0.8133 (t0) REVERT: B 60 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7522 (mm-40) REVERT: B 89 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8120 (mm-40) REVERT: B 102 GLN cc_start: 0.7907 (pt0) cc_final: 0.7402 (mm110) REVERT: B 131 LYS cc_start: 0.7573 (ptmm) cc_final: 0.7283 (tttm) REVERT: B 150 GLU cc_start: 0.7073 (tp30) cc_final: 0.6606 (mp0) REVERT: B 190 MET cc_start: 0.7201 (tmm) cc_final: 0.6966 (tmm) REVERT: B 213 ASP cc_start: 0.6790 (p0) cc_final: 0.6510 (t0) REVERT: B 270 MET cc_start: 0.6371 (tpp) cc_final: 0.6046 (mmm) REVERT: B 397 ASN cc_start: 0.8226 (p0) cc_final: 0.7972 (p0) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.5343 time to fit residues: 63.5921 Evaluate side-chains 81 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN B 34 HIS C B 325 GLN B 401 HIS B 472 GLN B 552 GLN B 598 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.154907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.121071 restraints weight = 14030.826| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.79 r_work: 0.3083 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6688 Z= 0.182 Angle : 0.627 10.091 9102 Z= 0.321 Chirality : 0.045 0.363 964 Planarity : 0.005 0.051 1170 Dihedral : 4.233 16.908 859 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.95 % Favored : 95.79 % Rotamer: Outliers : 1.59 % Allowed : 9.38 % Favored : 89.03 % 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: 0.46 (0.30), residues: 785 helix: 1.42 (0.28), residues: 370 sheet: 0.80 (0.69), residues: 55 loop : -0.97 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 357 TYR 0.026 0.002 TYR B 183 PHE 0.036 0.002 PHE B 400 TRP 0.009 0.001 TRP B 477 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 ( 6676) covalent geometry : angle 0.61097 / 0.32 ( 9076) SS BOND : bond 0.00397 / 0.20 ( 4) SS BOND : angle 1.43470 / 0.72 ( 8) hydrogen bonds : bond 0.06566 / 4.17 ( 292) hydrogen bonds : angle 4.37731 / 3.10 ( 818) metal coordination : bond 0.00294 / 0.15 ( 2) link_NAG-ASN : bond 0.00614 / 0.32 ( 6) link_NAG-ASN : angle 3.11192 / 1.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.267 Fit side-chains REVERT: A 440 LYS cc_start: 0.8717 (mttm) cc_final: 0.8364 (mmtm) REVERT: A 444 LYS cc_start: 0.8488 (mtpt) cc_final: 0.8226 (mtpm) REVERT: B 131 LYS cc_start: 0.7455 (ptmm) cc_final: 0.7246 (tttm) REVERT: B 150 GLU cc_start: 0.6910 (tp30) cc_final: 0.6525 (mp0) REVERT: B 332 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8159 (ttp) outliers start: 11 outliers final: 3 residues processed: 98 average time/residue: 0.4802 time to fit residues: 49.5748 Evaluate side-chains 87 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 0.0980 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN B 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.156072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120771 restraints weight = 9813.121| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.40 r_work: 0.3185 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6688 Z= 0.140 Angle : 0.588 10.260 9102 Z= 0.296 Chirality : 0.044 0.370 964 Planarity : 0.004 0.049 1170 Dihedral : 4.096 16.715 859 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.57 % Favored : 96.17 % Rotamer: Outliers : 1.88 % Allowed : 11.83 % Favored : 86.29 % 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: 0.58 (0.30), residues: 785 helix: 1.60 (0.28), residues: 364 sheet: 0.71 (0.68), residues: 55 loop : -0.94 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.022 0.001 TYR B 183 PHE 0.023 0.001 PHE B 400 TRP 0.010 0.001 TRP B 477 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 6676) covalent geometry : angle 0.57093 / 0.29 ( 9076) SS BOND : bond 0.00198 / 0.09 ( 4) SS BOND : angle 1.35018 / 0.67 ( 8) hydrogen bonds : bond 0.05584 / 3.55 ( 292) hydrogen bonds : angle 4.22175 / 2.99 ( 818) metal coordination : bond 0.00183 / 0.09 ( 2) link_NAG-ASN : bond 0.00631 / 0.34 ( 6) link_NAG-ASN : angle 3.11770 / 2.00 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.169 Fit side-chains REVERT: A 346 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7508 (ptm160) REVERT: A 440 LYS cc_start: 0.8724 (mttm) cc_final: 0.8385 (mmtm) REVERT: A 444 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8305 (mtpm) REVERT: B 332 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8090 (ttt) outliers start: 13 outliers final: 6 residues processed: 91 average time/residue: 0.4763 time to fit residues: 45.7592 Evaluate side-chains 84 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN B 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.153628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116964 restraints weight = 9519.718| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.17 r_work: 0.3151 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6688 Z= 0.176 Angle : 0.621 10.137 9102 Z= 0.314 Chirality : 0.045 0.379 964 Planarity : 0.004 0.049 1170 Dihedral : 4.247 16.873 859 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.21 % Favored : 95.54 % Rotamer: Outliers : 2.16 % Allowed : 12.84 % Favored : 84.99 % 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: 0.40 (0.30), residues: 785 helix: 1.35 (0.27), residues: 370 sheet: 0.78 (0.67), residues: 55 loop : -0.99 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.018 0.002 TYR B 199 PHE 0.028 0.002 PHE B 400 TRP 0.010 0.001 TRP A 353 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 6676) covalent geometry : angle 0.60369 / 0.31 ( 9076) SS BOND : bond 0.00296 / 0.14 ( 4) SS BOND : angle 1.58969 / 0.79 ( 8) hydrogen bonds : bond 0.06363 / 4.04 ( 292) hydrogen bonds : angle 4.26312 / 3.02 ( 818) metal coordination : bond 0.00301 / 0.15 ( 2) link_NAG-ASN : bond 0.00610 / 0.33 ( 6) link_NAG-ASN : angle 3.20087 / 2.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 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 : 0.160 Fit side-chains REVERT: A 346 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7498 (ptm160) REVERT: A 440 LYS cc_start: 0.8747 (mttm) cc_final: 0.8410 (mmtm) REVERT: B 341 LYS cc_start: 0.7791 (mmmt) cc_final: 0.7198 (mmmt) outliers start: 15 outliers final: 8 residues processed: 90 average time/residue: 0.4995 time to fit residues: 47.6011 Evaluate side-chains 82 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN B 81 GLN B 472 GLN B 505 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.154951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119965 restraints weight = 9919.429| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.39 r_work: 0.3173 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6688 Z= 0.141 Angle : 0.591 10.238 9102 Z= 0.296 Chirality : 0.044 0.380 964 Planarity : 0.004 0.050 1170 Dihedral : 4.106 16.796 859 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.95 % Favored : 95.79 % Rotamer: Outliers : 1.59 % Allowed : 14.29 % Favored : 84.13 % 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: 0.52 (0.30), residues: 785 helix: 1.53 (0.28), residues: 364 sheet: 0.75 (0.68), residues: 55 loop : -0.96 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.017 0.001 TYR A 501 PHE 0.018 0.001 PHE B 400 TRP 0.009 0.001 TRP B 477 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6676) covalent geometry : angle 0.57389 / 0.29 ( 9076) SS BOND : bond 0.00221 / 0.11 ( 4) SS BOND : angle 1.46159 / 0.73 ( 8) hydrogen bonds : bond 0.05515 / 3.50 ( 292) hydrogen bonds : angle 4.14520 / 2.93 ( 818) metal coordination : bond 0.00178 / 0.09 ( 2) link_NAG-ASN : bond 0.00623 / 0.33 ( 6) link_NAG-ASN : angle 3.14410 / 2.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.248 Fit side-chains REVERT: A 346 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7492 (ptm160) REVERT: A 440 LYS cc_start: 0.8749 (mttm) cc_final: 0.8415 (mmtm) REVERT: B 341 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7154 (mmmt) outliers start: 11 outliers final: 8 residues processed: 83 average time/residue: 0.5236 time to fit residues: 45.9074 Evaluate side-chains 81 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN B 81 GLN B 472 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.154256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110962 restraints weight = 18450.611| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.00 r_work: 0.3075 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6688 Z= 0.153 Angle : 0.601 10.199 9102 Z= 0.301 Chirality : 0.044 0.383 964 Planarity : 0.004 0.048 1170 Dihedral : 4.140 16.854 859 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.21 % Favored : 95.54 % Rotamer: Outliers : 2.02 % Allowed : 14.29 % Favored : 83.69 % 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: 0.51 (0.30), residues: 785 helix: 1.51 (0.27), residues: 364 sheet: 0.77 (0.67), residues: 55 loop : -0.95 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.017 0.001 TYR A 501 PHE 0.020 0.001 PHE B 400 TRP 0.009 0.001 TRP B 477 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 6676) covalent geometry : angle 0.58368 / 0.30 ( 9076) SS BOND : bond 0.00251 / 0.12 ( 4) SS BOND : angle 1.50055 / 0.74 ( 8) hydrogen bonds : bond 0.05808 / 3.68 ( 292) hydrogen bonds : angle 4.16351 / 2.94 ( 818) metal coordination : bond 0.00212 / 0.11 ( 2) link_NAG-ASN : bond 0.00610 / 0.33 ( 6) link_NAG-ASN : angle 3.17035 / 2.04 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.155 Fit side-chains REVERT: A 346 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7377 (ptm160) REVERT: A 440 LYS cc_start: 0.8742 (mttm) cc_final: 0.8401 (mmtm) REVERT: B 341 LYS cc_start: 0.7771 (mmmt) cc_final: 0.7075 (mmmt) outliers start: 14 outliers final: 10 residues processed: 84 average time/residue: 0.5271 time to fit residues: 46.5373 Evaluate side-chains 80 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113118 restraints weight = 15459.653| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.94 r_work: 0.3114 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6688 Z= 0.131 Angle : 0.587 10.278 9102 Z= 0.292 Chirality : 0.043 0.379 964 Planarity : 0.004 0.048 1170 Dihedral : 4.041 16.567 859 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.44 % Favored : 96.30 % Rotamer: Outliers : 2.02 % Allowed : 15.15 % Favored : 82.83 % 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: 0.62 (0.30), residues: 785 helix: 1.61 (0.28), residues: 364 sheet: 0.74 (0.67), residues: 55 loop : -0.89 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 357 TYR 0.016 0.001 TYR A 501 PHE 0.015 0.001 PHE B 400 TRP 0.010 0.001 TRP B 477 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 6676) covalent geometry : angle 0.56901 / 0.29 ( 9076) SS BOND : bond 0.00229 / 0.11 ( 4) SS BOND : angle 1.49288 / 0.74 ( 8) hydrogen bonds : bond 0.05219 / 3.31 ( 292) hydrogen bonds : angle 4.05277 / 2.86 ( 818) metal coordination : bond 0.00152 / 0.08 ( 2) link_NAG-ASN : bond 0.00615 / 0.33 ( 6) link_NAG-ASN : angle 3.14072 / 2.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.240 Fit side-chains REVERT: A 346 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7354 (ptm160) REVERT: A 440 LYS cc_start: 0.8754 (mttm) cc_final: 0.8373 (mmtm) REVERT: B 341 LYS cc_start: 0.7706 (mmmt) cc_final: 0.6985 (mmmt) outliers start: 14 outliers final: 9 residues processed: 80 average time/residue: 0.5332 time to fit residues: 44.8029 Evaluate side-chains 76 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 0.0050 chunk 72 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 0.0270 chunk 43 optimal weight: 0.7980 overall best weight: 0.5452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 228 HIS B 325 GLN B 472 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.157016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119337 restraints weight = 7753.643| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.06 r_work: 0.3183 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6688 Z= 0.119 Angle : 0.569 10.338 9102 Z= 0.281 Chirality : 0.043 0.372 964 Planarity : 0.004 0.047 1170 Dihedral : 3.888 16.195 859 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.06 % Favored : 96.68 % Rotamer: Outliers : 1.59 % Allowed : 15.15 % Favored : 83.26 % 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: 0.73 (0.31), residues: 785 helix: 1.74 (0.28), residues: 364 sheet: 0.75 (0.67), residues: 55 loop : -0.88 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.015 0.001 TYR A 501 PHE 0.012 0.001 PHE B 400 TRP 0.010 0.001 TRP B 477 HIS 0.009 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 6676) covalent geometry : angle 0.55184 / 0.28 ( 9076) SS BOND : bond 0.00197 / 0.10 ( 4) SS BOND : angle 1.26851 / 0.63 ( 8) hydrogen bonds : bond 0.04720 / 3.01 ( 292) hydrogen bonds : angle 3.98662 / 2.80 ( 818) metal coordination : bond 0.00119 / 0.06 ( 2) link_NAG-ASN : bond 0.00627 / 0.34 ( 6) link_NAG-ASN : angle 3.04902 / 1.97 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.209 Fit side-chains REVERT: A 346 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7441 (ptm160) REVERT: A 440 LYS cc_start: 0.8775 (mttm) cc_final: 0.8385 (mmtm) REVERT: B 341 LYS cc_start: 0.7720 (mmmt) cc_final: 0.6994 (mmmt) outliers start: 11 outliers final: 7 residues processed: 84 average time/residue: 0.5003 time to fit residues: 44.3720 Evaluate side-chains 78 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS B 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.156968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114366 restraints weight = 15550.242| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.93 r_work: 0.3112 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6688 Z= 0.128 Angle : 0.585 10.319 9102 Z= 0.291 Chirality : 0.043 0.370 964 Planarity : 0.004 0.046 1170 Dihedral : 3.890 16.261 859 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.57 % Favored : 96.17 % Rotamer: Outliers : 1.73 % Allowed : 15.87 % Favored : 82.40 % 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: 0.74 (0.31), residues: 785 helix: 1.76 (0.28), residues: 364 sheet: 0.72 (0.67), residues: 55 loop : -0.88 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.012 0.001 TYR B 516 PHE 0.014 0.001 PHE B 400 TRP 0.008 0.001 TRP B 566 HIS 0.011 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 6676) covalent geometry : angle 0.56879 / 0.29 ( 9076) SS BOND : bond 0.00217 / 0.11 ( 4) SS BOND : angle 1.32983 / 0.66 ( 8) hydrogen bonds : bond 0.04969 / 3.16 ( 292) hydrogen bonds : angle 4.01332 / 2.82 ( 818) metal coordination : bond 0.00143 / 0.07 ( 2) link_NAG-ASN : bond 0.00613 / 0.33 ( 6) link_NAG-ASN : angle 3.03675 / 1.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.248 Fit side-chains REVERT: A 346 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7345 (ptm160) REVERT: A 440 LYS cc_start: 0.8765 (mttm) cc_final: 0.8378 (mmtm) REVERT: B 341 LYS cc_start: 0.7688 (mmmt) cc_final: 0.6976 (mmmt) outliers start: 12 outliers final: 9 residues processed: 80 average time/residue: 0.5573 time to fit residues: 47.0499 Evaluate side-chains 80 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.0470 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 53 optimal weight: 0.4980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 228 HIS B 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.156392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115129 restraints weight = 11843.451| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.53 r_work: 0.3157 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6688 Z= 0.119 Angle : 0.569 10.340 9102 Z= 0.281 Chirality : 0.043 0.368 964 Planarity : 0.004 0.046 1170 Dihedral : 3.811 16.118 859 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.32 % Favored : 96.43 % Rotamer: Outliers : 1.44 % Allowed : 16.02 % Favored : 82.54 % 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: 0.79 (0.31), residues: 785 helix: 1.79 (0.28), residues: 365 sheet: 0.69 (0.67), residues: 55 loop : -0.84 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.011 0.001 TYR B 516 PHE 0.011 0.001 PHE B 400 TRP 0.010 0.001 TRP B 477 HIS 0.013 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 6676) covalent geometry : angle 0.55271 / 0.28 ( 9076) SS BOND : bond 0.00201 / 0.10 ( 4) SS BOND : angle 1.20407 / 0.59 ( 8) hydrogen bonds : bond 0.04601 / 2.92 ( 292) hydrogen bonds : angle 3.96796 / 2.79 ( 818) metal coordination : bond 0.00131 / 0.07 ( 2) link_NAG-ASN : bond 0.00610 / 0.33 ( 6) link_NAG-ASN : angle 2.99372 / 1.93 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.244 Fit side-chains REVERT: A 346 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7524 (ptm160) REVERT: A 440 LYS cc_start: 0.8797 (mttm) cc_final: 0.8391 (mmtm) REVERT: B 332 MET cc_start: 0.8216 (ttp) cc_final: 0.7993 (ttt) REVERT: B 341 LYS cc_start: 0.7721 (mmmt) cc_final: 0.6969 (mmmt) outliers start: 10 outliers final: 9 residues processed: 83 average time/residue: 0.5244 time to fit residues: 45.8858 Evaluate side-chains 85 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 0.0010 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 228 HIS B 472 GLN B 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.156678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.119989 restraints weight = 7661.107| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.91 r_work: 0.3226 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6688 Z= 0.128 Angle : 0.583 10.254 9102 Z= 0.290 Chirality : 0.043 0.366 964 Planarity : 0.004 0.046 1170 Dihedral : 3.855 16.028 859 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.57 % Favored : 96.17 % Rotamer: Outliers : 1.88 % Allowed : 15.58 % Favored : 82.54 % 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: 0.77 (0.31), residues: 785 helix: 1.77 (0.27), residues: 365 sheet: 0.67 (0.67), residues: 55 loop : -0.84 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.012 0.001 TYR B 516 PHE 0.014 0.001 PHE B 400 TRP 0.008 0.001 TRP B 477 HIS 0.016 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 6676) covalent geometry : angle 0.56745 / 0.29 ( 9076) SS BOND : bond 0.00207 / 0.10 ( 4) SS BOND : angle 1.30299 / 0.64 ( 8) hydrogen bonds : bond 0.04953 / 3.15 ( 292) hydrogen bonds : angle 3.98811 / 2.80 ( 818) metal coordination : bond 0.00147 / 0.07 ( 2) link_NAG-ASN : bond 0.00604 / 0.33 ( 6) link_NAG-ASN : angle 2.97823 / 1.92 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2477.77 seconds wall clock time: 42 minutes 58.01 seconds (2578.01 seconds total)