Starting phenix.real_space_refine on Thu Jun 5 14:36:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iuq_60912/06_2025/9iuq_60912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iuq_60912/06_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_60912/06_2025/9iuq_60912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iuq_60912/06_2025/9iuq_60912.map" model { file = "/net/cci-nas-00/data/ceres_data/9iuq_60912/06_2025/9iuq_60912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iuq_60912/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.24, per 1000 atoms: 1.29 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: 1.70 Conformation dependent library (CDL) restraints added in 936.2 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: 0.99 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: 3.77 Time building geometry restraints manager: 2.03 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: 23.230 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 26.880 Find NCS groups from input model: 0.090 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.170 ------------------------------------------------------------------------------- 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 : 1.014 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: 0.2033 time to fit residues: 30.9127 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 : 1.317 ------------------------------------------------------------------------------- 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 = 0.121661 restraints weight = 7190.518| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.86 r_work: 0.3163 rms_B_bonded: 2.69 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 1.04614 ( 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 : 0.803 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6934 (mt-10) REVERT: A 89 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8117 (tm-30) REVERT: A 188 ASN cc_start: 0.7188 (OUTLIER) cc_final: 0.6920 (t0) REVERT: A 483 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: A 534 LYS cc_start: 0.8385 (mmmt) cc_final: 0.7720 (mttt) REVERT: A 558 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8083 (mp) outliers start: 25 outliers final: 9 residues processed: 98 average time/residue: 0.1830 time to fit residues: 25.6012 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 : 0.806 ------------------------------------------------------------------------------- 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: 0.9980 chunk 66 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 52 optimal weight: 0.0970 chunk 1 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.148830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.116987 restraints weight = 7333.807| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.90 r_work: 0.3070 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6593 Z= 0.117 Angle : 0.517 7.037 8969 Z= 0.256 Chirality : 0.040 0.128 938 Planarity : 0.004 0.063 1156 Dihedral : 4.990 55.155 893 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.32 % Allowed : 24.93 % Favored : 72.75 % 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: -0.25 (1.00), residues: 33 loop : -0.42 (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 0.00396 ( 2) link_NAG-ASN : angle 2.29478 ( 6) hydrogen bonds : bond 0.04411 ( 306) hydrogen bonds : angle 4.04332 ( 879) SS BOND : bond 0.00319 ( 6) SS BOND : angle 0.60192 ( 12) covalent geometry : bond 0.00264 ( 6585) covalent geometry : angle 0.51402 ( 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 90 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6434 (mt-10) REVERT: A 89 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8170 (tm-30) REVERT: A 188 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.7120 (t0) REVERT: A 534 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8046 (mtmt) REVERT: B 465 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8200 (mt-10) outliers start: 16 outliers final: 9 residues processed: 87 average time/residue: 0.1544 time to fit residues: 19.2353 Evaluate side-chains 80 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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: 0.4980 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.143618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.110641 restraints weight = 7366.340| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.86 r_work: 0.2986 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6593 Z= 0.138 Angle : 0.522 6.960 8969 Z= 0.262 Chirality : 0.040 0.135 938 Planarity : 0.004 0.059 1156 Dihedral : 4.941 55.310 891 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.61 % Allowed : 25.07 % 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: 0.76 (0.31), residues: 780 helix: 1.45 (0.27), residues: 399 sheet: -0.21 (0.98), residues: 33 loop : -0.49 (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 401 PHE 0.014 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 2) link_NAG-ASN : angle 1.90266 ( 6) hydrogen bonds : bond 0.04696 ( 306) hydrogen bonds : angle 3.98748 ( 879) SS BOND : bond 0.00310 ( 6) SS BOND : angle 0.67272 ( 12) covalent geometry : bond 0.00326 ( 6585) covalent geometry : angle 0.51938 ( 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 92 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6465 (mt-10) REVERT: A 89 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8117 (tm-30) REVERT: A 267 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8465 (tt) REVERT: A 534 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8137 (mtmt) outliers start: 18 outliers final: 14 residues processed: 88 average time/residue: 0.1736 time to fit residues: 20.8950 Evaluate side-chains 86 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 347 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 371 PHE Chi-restraints excluded: chain B residue 393 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 0.0070 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 0.0770 chunk 26 optimal weight: 0.0270 chunk 15 optimal weight: 3.9990 overall best weight: 0.2814 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.147717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115128 restraints weight = 7271.598| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.84 r_work: 0.3175 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3082 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= 0.095 Angle : 0.481 8.932 8969 Z= 0.238 Chirality : 0.038 0.135 938 Planarity : 0.004 0.053 1156 Dihedral : 4.725 53.810 891 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.46 % Allowed : 24.93 % 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: 0.98 (0.31), residues: 780 helix: 1.62 (0.27), residues: 398 sheet: 0.08 (0.98), residues: 33 loop : -0.39 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.002 0.000 HIS A 505 PHE 0.009 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.001 0.000 ARG A 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 2) link_NAG-ASN : angle 1.62890 ( 6) hydrogen bonds : bond 0.03849 ( 306) hydrogen bonds : angle 3.90781 ( 879) SS BOND : bond 0.00120 ( 6) SS BOND : angle 0.49110 ( 12) covalent geometry : bond 0.00202 ( 6585) covalent geometry : angle 0.47883 ( 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 90 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6294 (mt-10) REVERT: A 192 ARG cc_start: 0.7689 (mmt-90) cc_final: 0.7385 (mmt180) REVERT: A 267 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8334 (tt) REVERT: A 534 LYS cc_start: 0.8583 (mmmt) cc_final: 0.8102 (mtmt) REVERT: B 465 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8154 (mt-10) outliers start: 17 outliers final: 13 residues processed: 88 average time/residue: 0.1398 time to fit residues: 17.9156 Evaluate side-chains 82 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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 579 MET 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 Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 0.0570 chunk 32 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.0020 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.3906 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.147389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115011 restraints weight = 7226.013| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.86 r_work: 0.3089 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3229 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= 0.101 Angle : 0.478 5.680 8969 Z= 0.239 Chirality : 0.039 0.135 938 Planarity : 0.004 0.051 1156 Dihedral : 4.706 54.336 891 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.19 % Allowed : 24.49 % 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: 1.06 (0.31), residues: 780 helix: 1.64 (0.27), residues: 400 sheet: 0.22 (0.93), residues: 33 loop : -0.32 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.000 HIS A 540 PHE 0.011 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.001 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 2) link_NAG-ASN : angle 1.57436 ( 6) hydrogen bonds : bond 0.03974 ( 306) hydrogen bonds : angle 3.84815 ( 879) SS BOND : bond 0.00164 ( 6) SS BOND : angle 0.48755 ( 12) covalent geometry : bond 0.00224 ( 6585) covalent geometry : angle 0.47620 ( 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 91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6278 (mt-10) REVERT: A 89 GLN cc_start: 0.8709 (mm110) cc_final: 0.8273 (tm-30) REVERT: A 534 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8082 (mtmt) outliers start: 22 outliers final: 17 residues processed: 86 average time/residue: 0.1393 time to fit residues: 17.4608 Evaluate side-chains 84 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 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 A residue 579 MET 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 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.143012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.110194 restraints weight = 7294.701| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.86 r_work: 0.2991 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6593 Z= 0.138 Angle : 0.541 14.571 8969 Z= 0.265 Chirality : 0.040 0.134 938 Planarity : 0.004 0.050 1156 Dihedral : 4.845 55.653 891 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.48 % Allowed : 23.77 % Favored : 72.75 % 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: 0.94 (0.31), residues: 780 helix: 1.61 (0.27), residues: 397 sheet: 0.35 (0.93), residues: 33 loop : -0.47 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.003 0.001 HIS A 401 PHE 0.014 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00128 ( 2) link_NAG-ASN : angle 1.91927 ( 6) hydrogen bonds : bond 0.04569 ( 306) hydrogen bonds : angle 3.90299 ( 879) SS BOND : bond 0.00241 ( 6) SS BOND : angle 0.67643 ( 12) covalent geometry : bond 0.00326 ( 6585) covalent geometry : angle 0.53819 ( 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 94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6398 (mt-10) REVERT: A 255 TYR cc_start: 0.7651 (m-80) cc_final: 0.6974 (m-80) REVERT: A 465 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8330 (ptpt) REVERT: A 534 LYS cc_start: 0.8686 (mmmt) cc_final: 0.8112 (mtmt) REVERT: B 465 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8162 (mt-10) outliers start: 24 outliers final: 18 residues processed: 90 average time/residue: 0.1498 time to fit residues: 19.0481 Evaluate side-chains 90 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 212 VAL Chi-restraints excluded: chain A residue 231 GLU 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 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 368 LEU 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: 2.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 68 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.143895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.111145 restraints weight = 7275.984| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.88 r_work: 0.3000 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3497 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= 0.120 Angle : 0.529 13.255 8969 Z= 0.258 Chirality : 0.040 0.135 938 Planarity : 0.004 0.049 1156 Dihedral : 4.822 54.665 891 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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: 0.97 (0.31), residues: 780 helix: 1.62 (0.27), residues: 397 sheet: 0.34 (0.91), residues: 33 loop : -0.42 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.003 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 0.00107 ( 2) link_NAG-ASN : angle 1.83371 ( 6) hydrogen bonds : bond 0.04284 ( 306) hydrogen bonds : angle 3.88710 ( 879) SS BOND : bond 0.00212 ( 6) SS BOND : angle 0.60039 ( 12) covalent geometry : bond 0.00277 ( 6585) covalent geometry : angle 0.52655 ( 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 94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.699 Fit side-chains REVERT: A 23 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6326 (mt-10) REVERT: A 255 TYR cc_start: 0.7655 (m-80) cc_final: 0.6983 (m-80) REVERT: A 534 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8112 (mtmt) REVERT: B 465 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8130 (mt-10) outliers start: 25 outliers final: 19 residues processed: 88 average time/residue: 0.1580 time to fit residues: 19.7003 Evaluate side-chains 89 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU 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 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 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: 0.9990 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.142495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.109900 restraints weight = 7361.405| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.87 r_work: 0.2997 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3574 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= 0.131 Angle : 0.549 12.539 8969 Z= 0.266 Chirality : 0.040 0.135 938 Planarity : 0.004 0.049 1156 Dihedral : 4.879 55.195 891 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.77 % Allowed : 23.48 % Favored : 72.75 % 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: 0.94 (0.31), residues: 780 helix: 1.58 (0.27), residues: 397 sheet: 0.39 (0.89), residues: 33 loop : -0.43 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.003 0.001 HIS A 401 PHE 0.013 0.001 PHE A 523 TYR 0.018 0.001 TYR A 252 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00112 ( 2) link_NAG-ASN : angle 1.89224 ( 6) hydrogen bonds : bond 0.04470 ( 306) hydrogen bonds : angle 3.91375 ( 879) SS BOND : bond 0.00248 ( 6) SS BOND : angle 0.91218 ( 12) covalent geometry : bond 0.00306 ( 6585) covalent geometry : angle 0.54594 ( 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 97 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.742 Fit side-chains REVERT: A 23 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6372 (mt-10) REVERT: A 255 TYR cc_start: 0.7649 (m-80) cc_final: 0.6978 (m-80) REVERT: A 483 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: A 534 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8115 (mtmt) REVERT: B 465 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8150 (mt-10) outliers start: 26 outliers final: 19 residues processed: 92 average time/residue: 0.1514 time to fit residues: 19.7155 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 : 0.718 ------------------------------------------------------------------------------- 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 188 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 231 GLU 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 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 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: 0.0570 chunk 56 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.143005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.110396 restraints weight = 7329.278| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.89 r_work: 0.3004 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3606 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= 0.118 Angle : 0.543 12.484 8969 Z= 0.263 Chirality : 0.040 0.137 938 Planarity : 0.004 0.048 1156 Dihedral : 4.847 54.754 891 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.33 % Allowed : 23.77 % Favored : 72.90 % 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: 0.99 (0.31), residues: 780 helix: 1.60 (0.27), residues: 397 sheet: 0.59 (0.89), 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 0.012 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 0.00111 ( 2) link_NAG-ASN : angle 1.84495 ( 6) hydrogen bonds : bond 0.04311 ( 306) hydrogen bonds : angle 3.89257 ( 879) SS BOND : bond 0.00229 ( 6) SS BOND : angle 0.77361 ( 12) covalent geometry : bond 0.00270 ( 6585) covalent geometry : angle 0.54028 ( 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 92 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 2.145 Fit side-chains REVERT: A 23 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6306 (mt-10) REVERT: A 483 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: A 534 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8116 (mtmt) REVERT: B 465 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8128 (mt-10) outliers start: 23 outliers final: 18 residues processed: 88 average time/residue: 0.2677 time to fit residues: 32.4183 Evaluate side-chains 92 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 2.287 ------------------------------------------------------------------------------- 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 212 VAL Chi-restraints excluded: chain A residue 231 GLU 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 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 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: 0.8980 chunk 65 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.142159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.109290 restraints weight = 7491.547| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.90 r_work: 0.2977 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6593 Z= 0.135 Angle : 0.559 12.063 8969 Z= 0.272 Chirality : 0.041 0.137 938 Planarity : 0.004 0.048 1156 Dihedral : 4.909 55.464 891 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.19 % Allowed : 24.06 % Favored : 72.75 % 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: 1.55 (0.27), residues: 397 sheet: 0.60 (0.89), residues: 33 loop : -0.44 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.003 0.001 HIS A 540 PHE 0.013 0.001 PHE A 523 TYR 0.017 0.001 TYR A 385 ARG 0.003 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00120 ( 2) link_NAG-ASN : angle 1.94912 ( 6) hydrogen bonds : bond 0.04569 ( 306) hydrogen bonds : angle 3.92330 ( 879) SS BOND : bond 0.00260 ( 6) SS BOND : angle 0.80011 ( 12) covalent geometry : bond 0.00319 ( 6585) covalent geometry : angle 0.55629 ( 8951) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5648.14 seconds wall clock time: 100 minutes 58.09 seconds (6058.09 seconds total)