Starting phenix.real_space_refine on Sat May 10 13:44:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iuq_60912/05_2025/9iuq_60912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iuq_60912/05_2025/9iuq_60912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iuq_60912/05_2025/9iuq_60912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iuq_60912/05_2025/9iuq_60912.map" model { file = "/net/cci-nas-00/data/ceres_data/9iuq_60912/05_2025/9iuq_60912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iuq_60912/05_2025/9iuq_60912.cif" } resolution = 3.3 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= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4103 2.51 5 N 1059 2.21 5 O 1201 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6399 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 27, 'TRANS': 566} Chain: "B" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1526 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 12, 'TRANS': 177} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.31, per 1000 atoms: 0.67 Number of scatterers: 6399 At special positions: 0 Unit cell: (76.26, 86.92, 118.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1201 8.00 N 1059 7.00 C 4103 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 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 B 601 " - " ASN B 343 " " NAG B 602 " - " ASN B 354 " Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 859.0 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1480 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 56.2% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.993A pdb=" N LYS A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.562A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.603A pdb=" N ASN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.566A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 Proline residue: A 235 - end of helix removed outlier: 3.907A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.551A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.769A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.847A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 removed outlier: 3.792A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 388 No H-bonds generated for 'chain 'A' and resid 387 through 388' Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.551A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.780A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 473 through 484 removed outlier: 3.625A pdb=" N TRP A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 532 removed outlier: 4.416A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.533A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.656A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.534A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.710A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.602A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.526A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.577A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 451 through 454 removed outlier: 4.550A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 306 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1062 1.31 - 1.44: 1915 1.44 - 1.56: 3549 1.56 - 1.69: 2 1.69 - 1.81: 57 Bond restraints: 6585 Sorted by residual: bond pdb=" C HIS A 34 " pdb=" O HIS A 34 " ideal model delta sigma weight residual 1.236 1.348 -0.112 1.15e-02 7.56e+03 9.41e+01 bond pdb=" C LYS A 31 " pdb=" O LYS A 31 " ideal model delta sigma weight residual 1.237 1.306 -0.069 1.17e-02 7.31e+03 3.47e+01 bond pdb=" CA SER A 44 " pdb=" CB SER A 44 " ideal model delta sigma weight residual 1.528 1.438 0.090 1.59e-02 3.96e+03 3.24e+01 bond pdb=" C ASP A 30 " pdb=" O ASP A 30 " ideal model delta sigma weight residual 1.237 1.302 -0.065 1.16e-02 7.43e+03 3.19e+01 bond pdb=" CA ALA A 36 " pdb=" CB ALA A 36 " ideal model delta sigma weight residual 1.529 1.444 0.085 1.58e-02 4.01e+03 2.92e+01 ... (remaining 6580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 8793 3.06 - 6.11: 140 6.11 - 9.17: 13 9.17 - 12.22: 3 12.22 - 15.28: 2 Bond angle restraints: 8951 Sorted by residual: angle pdb=" CA PRO A 469 " pdb=" N PRO A 469 " pdb=" CD PRO A 469 " ideal model delta sigma weight residual 112.00 96.72 15.28 1.40e+00 5.10e-01 1.19e+02 angle pdb=" C TYR A 41 " pdb=" CA TYR A 41 " pdb=" CB TYR A 41 " ideal model delta sigma weight residual 110.81 99.15 11.66 1.60e+00 3.91e-01 5.31e+01 angle pdb=" C HIS A 34 " pdb=" CA HIS A 34 " pdb=" CB HIS A 34 " ideal model delta sigma weight residual 110.96 100.96 10.00 1.54e+00 4.22e-01 4.22e+01 angle pdb=" CA PHE A 72 " pdb=" CB PHE A 72 " pdb=" CG PHE A 72 " ideal model delta sigma weight residual 113.80 119.81 -6.01 1.00e+00 1.00e+00 3.61e+01 angle pdb=" N TYR A 41 " pdb=" CA TYR A 41 " pdb=" CB TYR A 41 " ideal model delta sigma weight residual 109.94 118.49 -8.55 1.49e+00 4.50e-01 3.29e+01 ... (remaining 8946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3236 17.70 - 35.39: 493 35.39 - 53.09: 134 53.09 - 70.79: 38 70.79 - 88.48: 7 Dihedral angle restraints: 3908 sinusoidal: 1604 harmonic: 2304 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 165.66 -72.66 1 1.00e+01 1.00e-02 6.74e+01 dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 138.28 -45.28 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" C PHE A 28 " pdb=" N PHE A 28 " pdb=" CA PHE A 28 " pdb=" CB PHE A 28 " ideal model delta harmonic sigma weight residual -122.60 -109.29 -13.31 0 2.50e+00 1.60e-01 2.84e+01 ... (remaining 3905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 788 0.056 - 0.113: 129 0.113 - 0.169: 15 0.169 - 0.226: 5 0.226 - 0.282: 1 Chirality restraints: 938 Sorted by residual: chirality pdb=" CA PHE A 28 " pdb=" N PHE A 28 " pdb=" C PHE A 28 " pdb=" CB PHE A 28 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE B 358 " pdb=" CA ILE B 358 " pdb=" CG1 ILE B 358 " pdb=" CG2 ILE B 358 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA SER A 47 " pdb=" N SER A 47 " pdb=" C SER A 47 " pdb=" CB SER A 47 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.62e-01 ... (remaining 935 not shown) Planarity restraints: 1158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 468 " -0.113 5.00e-02 4.00e+02 1.58e-01 3.97e+01 pdb=" N PRO A 469 " 0.272 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " 0.071 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO A 235 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 37 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.96e+00 pdb=" C GLU A 37 " -0.052 2.00e-02 2.50e+03 pdb=" O GLU A 37 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP A 38 " 0.018 2.00e-02 2.50e+03 ... (remaining 1155 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1475 2.78 - 3.31: 5771 3.31 - 3.84: 10145 3.84 - 4.37: 11532 4.37 - 4.90: 20844 Nonbonded interactions: 49767 Sorted by model distance: nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.253 3.120 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.264 3.040 nonbonded pdb=" O LEU A 278 " pdb=" OG1 THR A 282 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.304 3.040 nonbonded pdb=" OG SER A 155 " pdb=" OE2 GLU A 160 " model vdw 2.309 3.040 ... (remaining 49762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 18.080 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.158 6593 Z= 0.397 Angle : 0.837 15.280 8969 Z= 0.546 Chirality : 0.045 0.282 938 Planarity : 0.007 0.158 1156 Dihedral : 18.192 88.483 2410 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.72 % Allowed : 27.10 % Favored : 72.17 % Cbeta Deviations : 0.27 % 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: 0.27 (0.31), residues: 780 helix: 1.07 (0.28), residues: 375 sheet: -0.97 (1.00), residues: 34 loop : -0.58 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 69 HIS 0.009 0.001 HIS A 34 PHE 0.021 0.001 PHE A 72 TYR 0.018 0.001 TYR A 41 ARG 0.001 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00056 ( 2) link_NAG-ASN : angle 1.40477 ( 6) hydrogen bonds : bond 0.16883 ( 306) hydrogen bonds : angle 6.47728 ( 879) SS BOND : bond 0.00181 ( 6) SS BOND : angle 1.05407 ( 12) covalent geometry : bond 0.00598 ( 6585) covalent geometry : angle 0.83612 ( 8951) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.757 Fit side-chains REVERT: A 297 MET cc_start: 0.7921 (mtm) cc_final: 0.7687 (mtp) outliers start: 5 outliers final: 4 residues processed: 105 average time/residue: 0.1616 time to fit residues: 23.6231 Evaluate side-chains 85 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 0.0170 chunk 70 optimal weight: 3.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.152899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121649 restraints weight = 7190.501| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.86 r_work: 0.3162 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6593 Z= 0.124 Angle : 0.539 9.066 8969 Z= 0.271 Chirality : 0.040 0.195 938 Planarity : 0.005 0.074 1156 Dihedral : 5.401 55.206 897 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.62 % Allowed : 24.49 % Favored : 71.88 % 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: 0.64 (0.31), residues: 780 helix: 1.34 (0.27), residues: 391 sheet: -0.55 (1.01), residues: 34 loop : -0.46 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS A 540 PHE 0.025 0.001 PHE A 32 TYR 0.017 0.001 TYR A 385 ARG 0.005 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 2) link_NAG-ASN : angle 1.04615 ( 6) hydrogen bonds : bond 0.04762 ( 306) hydrogen bonds : angle 4.21274 ( 879) SS BOND : bond 0.00296 ( 6) SS BOND : angle 0.82626 ( 12) covalent geometry : bond 0.00286 ( 6585) covalent geometry : angle 0.53775 ( 8951) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6934 (mt-10) REVERT: A 89 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8116 (tm-30) REVERT: A 188 ASN cc_start: 0.7186 (OUTLIER) cc_final: 0.6917 (t0) REVERT: A 483 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: A 534 LYS cc_start: 0.8384 (mmmt) cc_final: 0.7719 (mttt) REVERT: A 558 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8084 (mp) outliers start: 25 outliers final: 9 residues processed: 98 average time/residue: 0.1589 time to fit residues: 21.7210 Evaluate side-chains 83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.148499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.116461 restraints weight = 7343.316| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.86 r_work: 0.3083 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6593 Z= 0.119 Angle : 0.514 6.862 8969 Z= 0.256 Chirality : 0.040 0.133 938 Planarity : 0.004 0.062 1156 Dihedral : 5.027 55.240 893 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.32 % Allowed : 25.22 % Favored : 72.46 % 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: 0.82 (0.32), residues: 780 helix: 1.48 (0.27), residues: 398 sheet: -0.21 (1.00), residues: 33 loop : -0.43 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS A 401 PHE 0.012 0.001 PHE A 523 TYR 0.019 0.001 TYR A 385 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 2) link_NAG-ASN : angle 2.05270 ( 6) hydrogen bonds : bond 0.04443 ( 306) hydrogen bonds : angle 4.04997 ( 879) SS BOND : bond 0.00402 ( 6) SS BOND : angle 0.59469 ( 12) covalent geometry : bond 0.00268 ( 6585) covalent geometry : angle 0.51130 ( 8951) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6450 (mt-10) REVERT: A 89 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8180 (tm-30) REVERT: A 188 ASN cc_start: 0.7401 (OUTLIER) cc_final: 0.7117 (t0) REVERT: A 534 LYS cc_start: 0.8532 (mmmt) cc_final: 0.8038 (mtmt) REVERT: B 465 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8176 (mt-10) outliers start: 16 outliers final: 9 residues processed: 88 average time/residue: 0.1452 time to fit residues: 18.3208 Evaluate side-chains 81 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 465 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.143121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.110192 restraints weight = 7370.352| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.90 r_work: 0.2988 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6593 Z= 0.147 Angle : 0.531 8.127 8969 Z= 0.266 Chirality : 0.041 0.140 938 Planarity : 0.004 0.058 1156 Dihedral : 4.970 55.746 891 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.61 % Allowed : 24.78 % Favored : 72.61 % 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: 780 helix: 1.39 (0.27), residues: 399 sheet: -0.15 (0.99), residues: 33 loop : -0.50 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS A 540 PHE 0.014 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.004 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 2) link_NAG-ASN : angle 2.03564 ( 6) hydrogen bonds : bond 0.04813 ( 306) hydrogen bonds : angle 4.02607 ( 879) SS BOND : bond 0.00247 ( 6) SS BOND : angle 0.79359 ( 12) covalent geometry : bond 0.00349 ( 6585) covalent geometry : angle 0.52797 ( 8951) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6529 (mt-10) REVERT: A 89 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8152 (tm-30) REVERT: A 169 ARG cc_start: 0.8232 (mmt-90) cc_final: 0.7958 (mmt-90) REVERT: A 267 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8499 (tt) REVERT: A 534 LYS cc_start: 0.8689 (mmmt) cc_final: 0.8140 (mtmt) outliers start: 18 outliers final: 13 residues processed: 89 average time/residue: 0.1668 time to fit residues: 20.3730 Evaluate side-chains 86 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.0970 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 chunk 26 optimal weight: 0.1980 chunk 15 optimal weight: 5.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.145283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.112665 restraints weight = 7289.128| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.87 r_work: 0.3017 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6593 Z= 0.108 Angle : 0.499 8.797 8969 Z= 0.247 Chirality : 0.039 0.133 938 Planarity : 0.004 0.053 1156 Dihedral : 4.825 54.261 891 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.90 % Allowed : 24.64 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.31), residues: 780 helix: 1.51 (0.27), residues: 398 sheet: 0.07 (0.97), residues: 33 loop : -0.44 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.002 0.001 HIS A 401 PHE 0.011 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 2) link_NAG-ASN : angle 1.81945 ( 6) hydrogen bonds : bond 0.04201 ( 306) hydrogen bonds : angle 3.95063 ( 879) SS BOND : bond 0.00161 ( 6) SS BOND : angle 0.56549 ( 12) covalent geometry : bond 0.00241 ( 6585) covalent geometry : angle 0.49709 ( 8951) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6322 (mt-10) REVERT: A 267 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8369 (tt) REVERT: A 534 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8090 (mtmt) REVERT: B 465 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8132 (mt-10) outliers start: 20 outliers final: 15 residues processed: 88 average time/residue: 0.1403 time to fit residues: 17.7657 Evaluate side-chains 86 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 465 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 0.0050 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 0.0070 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.6014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN B 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.143749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.111094 restraints weight = 7247.702| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.85 r_work: 0.3002 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6593 Z= 0.118 Angle : 0.497 6.505 8969 Z= 0.248 Chirality : 0.039 0.133 938 Planarity : 0.004 0.051 1156 Dihedral : 4.832 54.952 891 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.19 % Allowed : 24.64 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.31), residues: 780 helix: 1.53 (0.27), residues: 398 sheet: 0.23 (0.96), residues: 33 loop : -0.43 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS A 540 PHE 0.012 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.002 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 2) link_NAG-ASN : angle 1.82227 ( 6) hydrogen bonds : bond 0.04325 ( 306) hydrogen bonds : angle 3.91707 ( 879) SS BOND : bond 0.00189 ( 6) SS BOND : angle 0.59483 ( 12) covalent geometry : bond 0.00271 ( 6585) covalent geometry : angle 0.49496 ( 8951) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6352 (mt-10) REVERT: A 89 GLN cc_start: 0.8689 (mm110) cc_final: 0.8250 (tm-30) REVERT: A 267 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8419 (tt) REVERT: A 534 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8102 (mtmt) REVERT: B 465 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8121 (mt-10) outliers start: 22 outliers final: 18 residues processed: 88 average time/residue: 0.1588 time to fit residues: 19.6794 Evaluate side-chains 91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 28 optimal weight: 0.0270 chunk 61 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.143703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.110946 restraints weight = 7286.972| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.87 r_work: 0.2998 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6593 Z= 0.118 Angle : 0.505 10.617 8969 Z= 0.250 Chirality : 0.039 0.135 938 Planarity : 0.004 0.049 1156 Dihedral : 4.834 54.874 891 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.62 % Allowed : 23.77 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.31), residues: 780 helix: 1.56 (0.27), residues: 398 sheet: 0.33 (0.94), residues: 33 loop : -0.44 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS A 401 PHE 0.012 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.002 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 2) link_NAG-ASN : angle 1.82194 ( 6) hydrogen bonds : bond 0.04280 ( 306) hydrogen bonds : angle 3.91155 ( 879) SS BOND : bond 0.00218 ( 6) SS BOND : angle 0.59417 ( 12) covalent geometry : bond 0.00270 ( 6585) covalent geometry : angle 0.50275 ( 8951) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6332 (mt-10) REVERT: A 267 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8307 (tt) REVERT: A 465 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7956 (ptpt) REVERT: A 534 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8109 (mtmt) REVERT: B 465 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8126 (mt-10) outliers start: 25 outliers final: 19 residues processed: 91 average time/residue: 0.1613 time to fit residues: 20.6908 Evaluate side-chains 92 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 0.0670 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.143969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.111361 restraints weight = 7303.968| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.87 r_work: 0.3004 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6593 Z= 0.111 Angle : 0.503 9.378 8969 Z= 0.249 Chirality : 0.039 0.135 938 Planarity : 0.004 0.048 1156 Dihedral : 4.792 54.450 891 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.91 % Allowed : 23.77 % Favored : 72.32 % 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: 0.98 (0.31), residues: 780 helix: 1.61 (0.27), residues: 398 sheet: 0.37 (0.92), residues: 33 loop : -0.41 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS A 401 PHE 0.011 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.002 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 2) link_NAG-ASN : angle 1.75803 ( 6) hydrogen bonds : bond 0.04165 ( 306) hydrogen bonds : angle 3.88959 ( 879) SS BOND : bond 0.00210 ( 6) SS BOND : angle 0.57140 ( 12) covalent geometry : bond 0.00251 ( 6585) covalent geometry : angle 0.50063 ( 8951) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6312 (mt-10) REVERT: A 267 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8260 (tt) REVERT: A 465 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7846 (ptpt) REVERT: A 534 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8093 (mtmt) REVERT: B 465 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8114 (mt-10) outliers start: 27 outliers final: 21 residues processed: 91 average time/residue: 0.1515 time to fit residues: 19.3722 Evaluate side-chains 93 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 0.1980 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.0570 chunk 40 optimal weight: 8.9990 chunk 31 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.0470 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.145632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.113235 restraints weight = 7314.273| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.86 r_work: 0.3045 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6593 Z= 0.098 Angle : 0.491 10.265 8969 Z= 0.243 Chirality : 0.039 0.136 938 Planarity : 0.004 0.047 1156 Dihedral : 4.722 53.802 891 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.91 % Allowed : 23.77 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.31), residues: 780 helix: 1.66 (0.27), residues: 400 sheet: 0.53 (0.91), residues: 33 loop : -0.32 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.002 0.000 HIS A 540 PHE 0.009 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 2) link_NAG-ASN : angle 1.61243 ( 6) hydrogen bonds : bond 0.03860 ( 306) hydrogen bonds : angle 3.86523 ( 879) SS BOND : bond 0.00169 ( 6) SS BOND : angle 0.50339 ( 12) covalent geometry : bond 0.00212 ( 6585) covalent geometry : angle 0.48892 ( 8951) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6151 (mt-10) REVERT: A 267 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8156 (tt) REVERT: A 465 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7882 (ptpt) REVERT: A 483 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: A 534 LYS cc_start: 0.8686 (mmmt) cc_final: 0.8050 (mtmt) REVERT: B 465 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8122 (mt-10) outliers start: 27 outliers final: 21 residues processed: 94 average time/residue: 0.1528 time to fit residues: 20.3456 Evaluate side-chains 97 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.1980 chunk 56 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.144814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.111349 restraints weight = 7289.330| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.84 r_work: 0.3031 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6593 Z= 0.115 Angle : 0.508 9.583 8969 Z= 0.253 Chirality : 0.039 0.140 938 Planarity : 0.004 0.048 1156 Dihedral : 4.751 54.551 891 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.91 % Allowed : 23.91 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.31), residues: 780 helix: 1.69 (0.27), residues: 397 sheet: 0.64 (0.91), residues: 33 loop : -0.40 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.002 0.001 HIS A 540 PHE 0.011 0.001 PHE A 523 TYR 0.020 0.001 TYR A 41 ARG 0.004 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 2) link_NAG-ASN : angle 1.65494 ( 6) hydrogen bonds : bond 0.04162 ( 306) hydrogen bonds : angle 3.86122 ( 879) SS BOND : bond 0.00206 ( 6) SS BOND : angle 0.56311 ( 12) covalent geometry : bond 0.00261 ( 6585) covalent geometry : angle 0.50616 ( 8951) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6251 (mt-10) REVERT: A 267 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8208 (tt) REVERT: A 465 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7842 (ptpt) REVERT: A 483 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: A 534 LYS cc_start: 0.8695 (mmmt) cc_final: 0.8061 (mtmt) REVERT: B 465 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8132 (mt-10) outliers start: 27 outliers final: 21 residues processed: 94 average time/residue: 0.1507 time to fit residues: 20.0046 Evaluate side-chains 93 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 63 optimal weight: 0.0170 chunk 54 optimal weight: 0.0020 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 0.4426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.144778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.112068 restraints weight = 7440.926| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.90 r_work: 0.3013 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6593 Z= 0.107 Angle : 0.504 9.778 8969 Z= 0.251 Chirality : 0.039 0.142 938 Planarity : 0.004 0.047 1156 Dihedral : 4.741 54.395 891 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.91 % Allowed : 23.62 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.31), residues: 780 helix: 1.70 (0.27), residues: 397 sheet: 0.74 (0.91), residues: 33 loop : -0.39 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS A 540 PHE 0.011 0.001 PHE A 523 TYR 0.019 0.001 TYR A 41 ARG 0.004 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 2) link_NAG-ASN : angle 1.63224 ( 6) hydrogen bonds : bond 0.04088 ( 306) hydrogen bonds : angle 3.85799 ( 879) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.54648 ( 12) covalent geometry : bond 0.00240 ( 6585) covalent geometry : angle 0.50231 ( 8951) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3795.45 seconds wall clock time: 66 minutes 39.46 seconds (3999.46 seconds total)