Starting phenix.real_space_refine on Thu Jul 24 19:38:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aqs_15588/07_2025/8aqs_15588.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aqs_15588/07_2025/8aqs_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8aqs_15588/07_2025/8aqs_15588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aqs_15588/07_2025/8aqs_15588.map" model { file = "/net/cci-nas-00/data/ceres_data/8aqs_15588/07_2025/8aqs_15588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aqs_15588/07_2025/8aqs_15588.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 3 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.08, per 1000 atoms: 1.09 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: 1.55 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.60 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: 2.06 Time building geometry restraints manager: 1.88 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 - 21.81: 3737 21.81 - 43.62: 229 43.62 - 65.43: 25 65.43 - 87.24: 9 87.24 - 109.05: 8 Dihedral angle restraints: 4008 sinusoidal: 1689 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=" C1 NAG B 905 " pdb=" C2 NAG B 905 " pdb=" C3 NAG B 905 " pdb=" O3 NAG B 905 " ideal model delta sinusoidal sigma weight residual -175.09 -66.04 -109.05 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C1 NAG B 905 " pdb=" C2 NAG B 905 " pdb=" C3 NAG B 905 " pdb=" C4 NAG B 905 " ideal model delta sinusoidal sigma weight residual -52.39 55.85 -108.24 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 4005 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: 3.210 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.040 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 : 14.740 109.048 2508 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (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 TRP 0.013 0.001 TRP B 477 HIS 0.003 0.001 HIS B 374 PHE 0.018 0.001 PHE B 400 TYR 0.020 0.001 TYR A 501 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00640 ( 6) link_NAG-ASN : angle 3.04197 ( 18) hydrogen bonds : bond 0.15023 ( 292) hydrogen bonds : angle 4.79337 ( 818) metal coordination : bond 0.00079 ( 2) SS BOND : bond 0.00134 ( 4) SS BOND : angle 0.54890 ( 8) covalent geometry : bond 0.00264 ( 6676) covalent geometry : angle 0.54345 ( 9076) *********************** 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 : 0.731 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: 0.6979 (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: 1.2011 time to fit residues: 142.8170 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 : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 5.9990 chunk 59 optimal weight: 0.0060 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3765 r_free = 0.3765 target = 0.154928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112495 restraints weight = 15058.279| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.77 r_work: 0.3087 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6688 Z= 0.190 Angle : 0.641 10.126 9102 Z= 0.326 Chirality : 0.046 0.383 964 Planarity : 0.005 0.049 1170 Dihedral : 8.351 75.618 985 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.83 % Favored : 95.92 % Rotamer: Outliers : 1.44 % Allowed : 9.67 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.30), residues: 785 helix: 1.40 (0.28), residues: 370 sheet: 0.81 (0.69), residues: 55 loop : -0.99 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.005 0.001 HIS B 374 PHE 0.035 0.002 PHE B 400 TYR 0.026 0.002 TYR B 183 ARG 0.007 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 6) link_NAG-ASN : angle 3.21633 ( 18) hydrogen bonds : bond 0.06621 ( 292) hydrogen bonds : angle 4.38934 ( 818) metal coordination : bond 0.00304 ( 2) SS BOND : bond 0.00426 ( 4) SS BOND : angle 1.35939 ( 8) covalent geometry : bond 0.00453 ( 6676) covalent geometry : angle 0.62462 ( 9076) *********************** 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 101 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.721 Fit side-chains REVERT: A 440 LYS cc_start: 0.8745 (mttm) cc_final: 0.8405 (mmtm) REVERT: A 444 LYS cc_start: 0.8516 (mtpt) cc_final: 0.8240 (mtpm) REVERT: B 131 LYS cc_start: 0.7425 (ptmm) cc_final: 0.7190 (tttm) REVERT: B 150 GLU cc_start: 0.6929 (tp30) cc_final: 0.6502 (mp0) REVERT: B 213 ASP cc_start: 0.6969 (p0) cc_final: 0.6732 (t0) REVERT: B 287 GLN cc_start: 0.7296 (mm-40) cc_final: 0.7070 (pp30) REVERT: B 332 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8252 (ttp) outliers start: 10 outliers final: 3 residues processed: 96 average time/residue: 1.1509 time to fit residues: 116.8512 Evaluate side-chains 88 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 347 THR 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 15 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 472 GLN B 505 HIS 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 = 0.154316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117093 restraints weight = 9463.632| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.23 r_work: 0.3147 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6688 Z= 0.169 Angle : 0.632 10.145 9102 Z= 0.316 Chirality : 0.045 0.392 964 Planarity : 0.004 0.049 1170 Dihedral : 6.880 55.463 985 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.46 % Favored : 95.28 % Rotamer: Outliers : 1.88 % Allowed : 11.54 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.30), residues: 785 helix: 1.40 (0.27), residues: 364 sheet: 0.72 (0.69), residues: 55 loop : -1.03 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.005 0.001 HIS B 374 PHE 0.027 0.002 PHE B 400 TYR 0.023 0.002 TYR B 183 ARG 0.007 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00688 ( 6) link_NAG-ASN : angle 3.30635 ( 18) hydrogen bonds : bond 0.06241 ( 292) hydrogen bonds : angle 4.31106 ( 818) metal coordination : bond 0.00289 ( 2) SS BOND : bond 0.00307 ( 4) SS BOND : angle 1.54930 ( 8) covalent geometry : bond 0.00395 ( 6676) covalent geometry : angle 0.61364 ( 9076) *********************** 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 99 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.745 Fit side-chains REVERT: A 346 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7495 (ptm160) REVERT: A 440 LYS cc_start: 0.8780 (mttm) cc_final: 0.8412 (mmtm) REVERT: B 287 GLN cc_start: 0.7340 (mm-40) cc_final: 0.7056 (pp30) REVERT: B 341 LYS cc_start: 0.7755 (mmmt) cc_final: 0.7192 (mmmt) outliers start: 13 outliers final: 7 residues processed: 93 average time/residue: 1.3180 time to fit residues: 129.3043 Evaluate side-chains 86 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 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 35 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3778 r_free = 0.3778 target = 0.156160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122731 restraints weight = 15107.762| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 4.03 r_work: 0.3095 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1559 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 : 0.600 10.226 9102 Z= 0.296 Chirality : 0.044 0.393 964 Planarity : 0.004 0.050 1170 Dihedral : 6.222 55.048 985 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.95 % Favored : 95.79 % Rotamer: Outliers : 2.16 % Allowed : 12.70 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.30), residues: 785 helix: 1.49 (0.28), residues: 364 sheet: 0.75 (0.67), residues: 55 loop : -0.96 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 477 HIS 0.005 0.001 HIS B 374 PHE 0.021 0.001 PHE B 400 TYR 0.019 0.001 TYR B 50 ARG 0.006 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00662 ( 6) link_NAG-ASN : angle 3.32145 ( 18) hydrogen bonds : bond 0.05513 ( 292) hydrogen bonds : angle 4.18156 ( 818) metal coordination : bond 0.00187 ( 2) SS BOND : bond 0.00251 ( 4) SS BOND : angle 1.40056 ( 8) covalent geometry : bond 0.00320 ( 6676) covalent geometry : angle 0.58127 ( 9076) *********************** 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 96 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.753 Fit side-chains REVERT: A 346 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7452 (ptm160) REVERT: A 440 LYS cc_start: 0.8744 (mttm) cc_final: 0.8412 (mmtm) REVERT: A 458 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.7053 (ptmt) REVERT: B 341 LYS cc_start: 0.7740 (mmmt) cc_final: 0.7150 (mmmt) outliers start: 15 outliers final: 9 residues processed: 92 average time/residue: 1.2044 time to fit residues: 116.9728 Evaluate side-chains 88 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 52 THR 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 13 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3781 r_free = 0.3781 target = 0.156480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120498 restraints weight = 9850.284| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.18 r_work: 0.3178 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1625 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= 0.133 Angle : 0.589 10.270 9102 Z= 0.291 Chirality : 0.044 0.390 964 Planarity : 0.004 0.049 1170 Dihedral : 5.805 54.815 985 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.83 % Favored : 95.92 % Rotamer: Outliers : 2.45 % Allowed : 13.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.30), residues: 785 helix: 1.55 (0.28), residues: 364 sheet: 0.77 (0.68), residues: 55 loop : -0.93 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 477 HIS 0.004 0.001 HIS B 374 PHE 0.016 0.001 PHE B 400 TYR 0.016 0.001 TYR A 501 ARG 0.008 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 6) link_NAG-ASN : angle 3.23506 ( 18) hydrogen bonds : bond 0.05294 ( 292) hydrogen bonds : angle 4.11945 ( 818) metal coordination : bond 0.00149 ( 2) SS BOND : bond 0.00213 ( 4) SS BOND : angle 1.24659 ( 8) covalent geometry : bond 0.00301 ( 6676) covalent geometry : angle 0.57101 ( 9076) *********************** 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 95 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7508 (ptm160) REVERT: A 440 LYS cc_start: 0.8744 (mttm) cc_final: 0.8427 (mmtm) REVERT: A 458 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.7065 (ptmt) REVERT: B 341 LYS cc_start: 0.7791 (mmmt) cc_final: 0.7225 (mmmt) outliers start: 17 outliers final: 11 residues processed: 90 average time/residue: 1.1654 time to fit residues: 110.9051 Evaluate side-chains 86 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 52 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3781 r_free = 0.3781 target = 0.156300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120705 restraints weight = 15176.155| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.80 r_work: 0.3089 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6688 Z= 0.137 Angle : 0.597 10.263 9102 Z= 0.295 Chirality : 0.044 0.389 964 Planarity : 0.004 0.048 1170 Dihedral : 5.640 55.071 985 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.83 % Favored : 95.92 % Rotamer: Outliers : 2.16 % Allowed : 14.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.30), residues: 785 helix: 1.57 (0.28), residues: 364 sheet: 0.76 (0.67), residues: 55 loop : -0.91 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 477 HIS 0.004 0.001 HIS B 374 PHE 0.016 0.001 PHE B 400 TYR 0.016 0.001 TYR A 501 ARG 0.008 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 6) link_NAG-ASN : angle 3.19244 ( 18) hydrogen bonds : bond 0.05319 ( 292) hydrogen bonds : angle 4.07610 ( 818) metal coordination : bond 0.00155 ( 2) SS BOND : bond 0.00234 ( 4) SS BOND : angle 1.51036 ( 8) covalent geometry : bond 0.00312 ( 6676) covalent geometry : angle 0.57881 ( 9076) *********************** 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: 15 poor density : 73 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7386 (ptm160) REVERT: A 440 LYS cc_start: 0.8736 (mttm) cc_final: 0.8386 (mmtm) REVERT: A 458 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6969 (pttt) REVERT: B 341 LYS cc_start: 0.7715 (mmmt) cc_final: 0.7137 (mmmt) outliers start: 15 outliers final: 11 residues processed: 84 average time/residue: 1.2632 time to fit residues: 111.7269 Evaluate side-chains 84 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 458 LYS 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 47 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS B 325 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 = 0.3760 r_free = 0.3760 target = 0.154921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.117662 restraints weight = 9466.813| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.23 r_work: 0.3190 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1732 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= 0.133 Angle : 0.588 10.283 9102 Z= 0.291 Chirality : 0.043 0.388 964 Planarity : 0.004 0.047 1170 Dihedral : 5.490 55.047 985 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.83 % Favored : 95.92 % Rotamer: Outliers : 2.16 % Allowed : 15.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 785 helix: 1.64 (0.28), residues: 364 sheet: 0.75 (0.67), residues: 55 loop : -0.91 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 477 HIS 0.008 0.001 HIS B 228 PHE 0.015 0.001 PHE B 400 TYR 0.016 0.001 TYR A 501 ARG 0.009 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00651 ( 6) link_NAG-ASN : angle 3.14058 ( 18) hydrogen bonds : bond 0.05188 ( 292) hydrogen bonds : angle 4.04732 ( 818) metal coordination : bond 0.00196 ( 2) SS BOND : bond 0.00220 ( 4) SS BOND : angle 1.35401 ( 8) covalent geometry : bond 0.00299 ( 6676) covalent geometry : angle 0.57009 ( 9076) *********************** 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 90 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7527 (ptm160) REVERT: A 440 LYS cc_start: 0.8767 (mttm) cc_final: 0.8444 (mmtm) REVERT: B 341 LYS cc_start: 0.7833 (mmmt) cc_final: 0.7205 (mmmt) outliers start: 15 outliers final: 11 residues processed: 86 average time/residue: 1.4711 time to fit residues: 133.3757 Evaluate side-chains 81 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 52 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.0020 chunk 70 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 228 HIS B 472 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.158042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121443 restraints weight = 7677.100| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.93 r_work: 0.3244 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1751 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= 0.116 Angle : 0.565 10.362 9102 Z= 0.278 Chirality : 0.043 0.381 964 Planarity : 0.004 0.047 1170 Dihedral : 5.173 54.444 985 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.44 % Favored : 96.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.31), residues: 785 helix: 1.74 (0.28), residues: 365 sheet: 0.73 (0.67), residues: 55 loop : -0.89 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 477 HIS 0.008 0.001 HIS B 228 PHE 0.011 0.001 PHE B 400 TYR 0.015 0.001 TYR A 501 ARG 0.008 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00656 ( 6) link_NAG-ASN : angle 3.02574 ( 18) hydrogen bonds : bond 0.04615 ( 292) hydrogen bonds : angle 3.98004 ( 818) metal coordination : bond 0.00118 ( 2) SS BOND : bond 0.00207 ( 4) SS BOND : angle 1.14378 ( 8) covalent geometry : bond 0.00255 ( 6676) covalent geometry : angle 0.54797 ( 9076) *********************** 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 89 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 1.871 Fit side-chains REVERT: A 346 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7581 (ptm160) REVERT: A 440 LYS cc_start: 0.8732 (mttm) cc_final: 0.8431 (mmtm) REVERT: B 341 LYS cc_start: 0.7798 (mmmt) cc_final: 0.7235 (mmmt) outliers start: 10 outliers final: 7 residues processed: 86 average time/residue: 1.6966 time to fit residues: 155.2099 Evaluate side-chains 80 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 126 ILE Chi-restraints excluded: chain B residue 182 GLU 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 0 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 228 HIS B 472 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.153810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116183 restraints weight = 7750.733| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.03 r_work: 0.3165 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6688 Z= 0.158 Angle : 0.618 10.150 9102 Z= 0.309 Chirality : 0.045 0.390 964 Planarity : 0.004 0.047 1170 Dihedral : 5.469 56.114 985 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.21 % Favored : 95.54 % Rotamer: Outliers : 1.73 % Allowed : 16.45 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.30), residues: 785 helix: 1.62 (0.27), residues: 364 sheet: 0.71 (0.67), residues: 55 loop : -0.95 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.011 0.001 HIS B 228 PHE 0.020 0.002 PHE B 400 TYR 0.016 0.001 TYR B 385 ARG 0.009 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00725 ( 6) link_NAG-ASN : angle 3.11681 ( 18) hydrogen bonds : bond 0.05785 ( 292) hydrogen bonds : angle 4.13242 ( 818) metal coordination : bond 0.00253 ( 2) SS BOND : bond 0.00320 ( 4) SS BOND : angle 1.71875 ( 8) covalent geometry : bond 0.00369 ( 6676) covalent geometry : angle 0.60055 ( 9076) *********************** 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 84 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 2.205 Fit side-chains revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7454 (ptm160) REVERT: A 440 LYS cc_start: 0.8803 (mttm) cc_final: 0.8406 (mmtm) REVERT: B 341 LYS cc_start: 0.7748 (mmmt) cc_final: 0.7004 (mmmt) outliers start: 12 outliers final: 11 residues processed: 80 average time/residue: 2.2273 time to fit residues: 189.9625 Evaluate side-chains 82 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 2.159 ------------------------------------------------------------------------------- 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 52 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 228 HIS B 472 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.154962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112414 restraints weight = 14212.482| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.84 r_work: 0.3066 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 6688 Z= 0.193 Angle : 1.046 59.198 9102 Z= 0.607 Chirality : 0.048 0.547 964 Planarity : 0.004 0.046 1170 Dihedral : 5.478 56.069 985 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.21 % Favored : 95.54 % Rotamer: Outliers : 1.73 % Allowed : 16.45 % Favored : 81.82 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.30), residues: 785 helix: 1.62 (0.27), residues: 364 sheet: 0.70 (0.67), residues: 55 loop : -0.96 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.013 0.001 HIS B 228 PHE 0.020 0.001 PHE B 400 TYR 0.016 0.001 TYR B 385 ARG 0.008 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00683 ( 6) link_NAG-ASN : angle 3.11333 ( 18) hydrogen bonds : bond 0.05674 ( 292) hydrogen bonds : angle 4.10788 ( 818) metal coordination : bond 0.00186 ( 2) SS BOND : bond 0.00265 ( 4) SS BOND : angle 1.67514 ( 8) covalent geometry : bond 0.00405 ( 6676) covalent geometry : angle 1.03676 ( 9076) ********************** 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 82 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7363 (ptm160) REVERT: A 440 LYS cc_start: 0.8772 (mttm) cc_final: 0.8379 (mmtm) REVERT: B 341 LYS cc_start: 0.7696 (mmmt) cc_final: 0.6962 (mmmt) outliers start: 12 outliers final: 11 residues processed: 79 average time/residue: 2.5210 time to fit residues: 212.1862 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 : 1.096 ------------------------------------------------------------------------------- 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 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 52 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 14 optimal weight: 0.1980 chunk 71 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3767 r_free = 0.3767 target = 0.155094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114211 restraints weight = 10023.739| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.36 r_work: 0.3119 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 6688 Z= 0.193 Angle : 1.046 59.198 9102 Z= 0.607 Chirality : 0.048 0.547 964 Planarity : 0.004 0.046 1170 Dihedral : 5.478 56.069 985 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.21 % Favored : 95.54 % Rotamer: Outliers : 1.88 % Allowed : 16.16 % Favored : 81.96 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.30), residues: 785 helix: 1.62 (0.27), residues: 364 sheet: 0.70 (0.67), residues: 55 loop : -0.96 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.013 0.001 HIS B 228 PHE 0.020 0.001 PHE B 400 TYR 0.016 0.001 TYR B 385 ARG 0.008 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00683 ( 6) link_NAG-ASN : angle 3.11333 ( 18) hydrogen bonds : bond 0.05674 ( 292) hydrogen bonds : angle 4.10788 ( 818) metal coordination : bond 0.00186 ( 2) SS BOND : bond 0.00265 ( 4) SS BOND : angle 1.67514 ( 8) covalent geometry : bond 0.00405 ( 6676) covalent geometry : angle 1.03676 ( 9076) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6594.74 seconds wall clock time: 119 minutes 0.90 seconds (7140.90 seconds total)