Starting phenix.real_space_refine on Tue Feb 11 02:14:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cax_45406/02_2025/9cax_45406.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cax_45406/02_2025/9cax_45406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cax_45406/02_2025/9cax_45406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cax_45406/02_2025/9cax_45406.map" model { file = "/net/cci-nas-00/data/ceres_data/9cax_45406/02_2025/9cax_45406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cax_45406/02_2025/9cax_45406.cif" } resolution = 3.37 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= 0.039 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 15 5.16 5 C 2387 2.51 5 N 583 2.21 5 O 626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3611 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3611 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 25, 'TRANS': 444} Time building chain proxies: 3.02, per 1000 atoms: 0.84 Number of scatterers: 3611 At special positions: 0 Unit cell: (83.5278, 61.4175, 67.9687, 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 15 16.00 O 626 8.00 N 583 7.00 C 2387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 473.8 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 854 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 87.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 53 through 67 removed outlier: 3.590A pdb=" N LEU A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 58 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.538A pdb=" N GLY A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 102 through 132 removed outlier: 3.808A pdb=" N THR A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ALA A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 157 removed outlier: 3.926A pdb=" N GLY A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 164 through 193 removed outlier: 3.659A pdb=" N ILE A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) Proline residue: A 186 - end of helix removed outlier: 3.812A pdb=" N SER A 190 " --> pdb=" O PRO A 186 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 191 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 192 " --> pdb=" O TYR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 removed outlier: 4.122A pdb=" N GLN A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 4.407A pdb=" N PHE A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 236' Processing helix chain 'A' and resid 238 through 252 removed outlier: 3.579A pdb=" N ALA A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.533A pdb=" N LEU A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.619A pdb=" N LYS A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 299 removed outlier: 3.587A pdb=" N VAL A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.569A pdb=" N LEU A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 330 removed outlier: 3.551A pdb=" N VAL A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 328 " --> pdb=" O MET A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 352 through 370 removed outlier: 3.599A pdb=" N GLY A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 removed outlier: 4.057A pdb=" N GLY A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 405 removed outlier: 3.687A pdb=" N LEU A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 429 removed outlier: 3.685A pdb=" N SER A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 416 " --> pdb=" O PRO A 412 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 422 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 442 removed outlier: 3.516A pdb=" N ILE A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 477 removed outlier: 3.782A pdb=" N ILE A 452 " --> pdb=" O PRO A 448 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 462 " --> pdb=" O ASN A 458 " (cutoff:3.500A) Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 479 through 499 removed outlier: 4.130A pdb=" N VAL A 483 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE A 484 " --> pdb=" O CYS A 480 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 519 removed outlier: 3.515A pdb=" N LYS A 516 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 714 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: 1.00 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1096 1.34 - 1.46: 866 1.46 - 1.58: 1718 1.58 - 1.70: 0 1.70 - 1.81: 22 Bond restraints: 3702 Sorted by residual: bond pdb=" C ALA A 80 " pdb=" N PRO A 81 " ideal model delta sigma weight residual 1.334 1.407 -0.073 2.34e-02 1.83e+03 9.81e+00 bond pdb=" CB PHE A 370 " pdb=" CG PHE A 370 " ideal model delta sigma weight residual 1.502 1.535 -0.033 2.30e-02 1.89e+03 2.09e+00 bond pdb=" C ILE A 433 " pdb=" N PRO A 434 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.28e-02 6.10e+03 1.88e+00 bond pdb=" C VAL A 411 " pdb=" N PRO A 412 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.28e-02 6.10e+03 1.82e+00 bond pdb=" C ARG A 381 " pdb=" N PRO A 382 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.28e-02 6.10e+03 1.76e+00 ... (remaining 3697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 4880 2.20 - 4.39: 115 4.39 - 6.59: 38 6.59 - 8.78: 7 8.78 - 10.98: 4 Bond angle restraints: 5044 Sorted by residual: angle pdb=" C LYS A 503 " pdb=" N ASN A 504 " pdb=" CA ASN A 504 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 angle pdb=" N TRP A 231 " pdb=" CA TRP A 231 " pdb=" C TRP A 231 " ideal model delta sigma weight residual 109.81 118.14 -8.33 2.21e+00 2.05e-01 1.42e+01 angle pdb=" CB MET A 174 " pdb=" CG MET A 174 " pdb=" SD MET A 174 " ideal model delta sigma weight residual 112.70 123.68 -10.98 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C THR A 478 " pdb=" CA THR A 478 " pdb=" CB THR A 478 " ideal model delta sigma weight residual 109.24 115.16 -5.92 1.75e+00 3.27e-01 1.15e+01 angle pdb=" CA VAL A 282 " pdb=" CB VAL A 282 " pdb=" CG1 VAL A 282 " ideal model delta sigma weight residual 110.40 115.89 -5.49 1.70e+00 3.46e-01 1.04e+01 ... (remaining 5039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 1837 16.82 - 33.65: 244 33.65 - 50.47: 61 50.47 - 67.30: 9 67.30 - 84.12: 6 Dihedral angle restraints: 2157 sinusoidal: 817 harmonic: 1340 Sorted by residual: dihedral pdb=" CA HIS A 97 " pdb=" C HIS A 97 " pdb=" N GLY A 98 " pdb=" CA GLY A 98 " ideal model delta harmonic sigma weight residual -180.00 -158.70 -21.30 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA GLY A 98 " pdb=" C GLY A 98 " pdb=" N ARG A 99 " pdb=" CA ARG A 99 " ideal model delta harmonic sigma weight residual 180.00 160.56 19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLU A 376 " pdb=" C GLU A 376 " pdb=" N HIS A 377 " pdb=" CA HIS A 377 " ideal model delta harmonic sigma weight residual -180.00 -162.22 -17.78 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 2154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 399 0.045 - 0.090: 149 0.090 - 0.134: 36 0.134 - 0.179: 7 0.179 - 0.224: 4 Chirality restraints: 595 Sorted by residual: chirality pdb=" CA THR A 478 " pdb=" N THR A 478 " pdb=" C THR A 478 " pdb=" CB THR A 478 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ASN A 504 " pdb=" N ASN A 504 " pdb=" C ASN A 504 " pdb=" CB ASN A 504 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CG LEU A 290 " pdb=" CB LEU A 290 " pdb=" CD1 LEU A 290 " pdb=" CD2 LEU A 290 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.91e-01 ... (remaining 592 not shown) Planarity restraints: 625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 370 " 0.012 2.00e-02 2.50e+03 1.86e-02 6.05e+00 pdb=" CG PHE A 370 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 370 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 370 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 370 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 370 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 370 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 282 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C VAL A 282 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL A 282 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 283 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 230 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C THR A 230 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 230 " 0.014 2.00e-02 2.50e+03 pdb=" N TRP A 231 " 0.013 2.00e-02 2.50e+03 ... (remaining 622 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 697 2.77 - 3.30: 3581 3.30 - 3.83: 5971 3.83 - 4.37: 7169 4.37 - 4.90: 12180 Nonbonded interactions: 29598 Sorted by model distance: nonbonded pdb=" O ILE A 335 " pdb=" OG1 THR A 339 " model vdw 2.234 3.040 nonbonded pdb=" O SER A 511 " pdb=" OG SER A 515 " model vdw 2.239 3.040 nonbonded pdb=" O THR A 399 " pdb=" OG1 THR A 403 " model vdw 2.247 3.040 nonbonded pdb=" O LEU A 398 " pdb=" OG1 THR A 401 " model vdw 2.273 3.040 nonbonded pdb=" OG SER A 55 " pdb=" O THR A 275 " model vdw 2.274 3.040 ... (remaining 29593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.920 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.480 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 3702 Z= 0.279 Angle : 0.925 10.977 5044 Z= 0.459 Chirality : 0.050 0.224 595 Planarity : 0.007 0.052 625 Dihedral : 16.469 84.120 1303 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.49 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 26.61 % Favored : 73.39 % 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: -2.36 (0.34), residues: 468 helix: -1.55 (0.23), residues: 351 sheet: None (None), residues: 0 loop : -0.92 (0.59), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 231 HIS 0.002 0.001 HIS A 264 PHE 0.042 0.002 PHE A 370 TYR 0.026 0.002 TYR A 258 ARG 0.012 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.379 Fit side-chains REVERT: A 287 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8646 (mm-30) REVERT: A 288 GLU cc_start: 0.8547 (tp30) cc_final: 0.7991 (tp30) REVERT: A 292 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8134 (mt-10) REVERT: A 377 HIS cc_start: 0.7389 (m-70) cc_final: 0.6905 (t70) REVERT: A 410 TRP cc_start: 0.7637 (p-90) cc_final: 0.7298 (p-90) REVERT: A 435 PHE cc_start: 0.7734 (m-80) cc_final: 0.7412 (m-80) REVERT: A 438 THR cc_start: 0.8982 (m) cc_final: 0.8676 (p) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1421 time to fit residues: 10.2099 Evaluate side-chains 54 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.4980 chunk 35 optimal weight: 0.0470 chunk 19 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 203 GLN A 245 GLN A 333 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.166286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132326 restraints weight = 4781.561| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.87 r_work: 0.3438 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3702 Z= 0.205 Angle : 0.699 9.021 5044 Z= 0.355 Chirality : 0.043 0.147 595 Planarity : 0.005 0.032 625 Dihedral : 4.497 21.794 504 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.27 % Favored : 95.51 % Rotamer: Outliers : 1.81 % Allowed : 25.06 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.10 (0.38), residues: 468 helix: 0.22 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -0.74 (0.72), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 93 HIS 0.004 0.001 HIS A 97 PHE 0.023 0.002 PHE A 441 TYR 0.014 0.001 TYR A 258 ARG 0.003 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.426 Fit side-chains REVERT: A 97 HIS cc_start: 0.7252 (OUTLIER) cc_final: 0.6570 (p-80) REVERT: A 287 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8730 (mm-30) REVERT: A 288 GLU cc_start: 0.8702 (tp30) cc_final: 0.8206 (tp30) REVERT: A 292 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8193 (mt-10) REVERT: A 377 HIS cc_start: 0.7559 (m-70) cc_final: 0.7168 (t70) REVERT: A 438 THR cc_start: 0.8927 (m) cc_final: 0.8552 (p) outliers start: 7 outliers final: 2 residues processed: 72 average time/residue: 0.1287 time to fit residues: 12.0583 Evaluate side-chains 64 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 374 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN A 333 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.161607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127340 restraints weight = 4731.046| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.84 r_work: 0.3378 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3702 Z= 0.240 Angle : 0.665 8.872 5044 Z= 0.335 Chirality : 0.043 0.148 595 Planarity : 0.004 0.026 625 Dihedral : 4.435 22.399 504 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.27 % Favored : 95.51 % Rotamer: Outliers : 1.81 % Allowed : 25.32 % Favored : 72.87 % 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: 0.74 (0.40), residues: 468 helix: 0.90 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.80 (0.67), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 93 HIS 0.004 0.001 HIS A 97 PHE 0.019 0.002 PHE A 441 TYR 0.014 0.001 TYR A 258 ARG 0.002 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.475 Fit side-chains REVERT: A 97 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.7254 (p-80) REVERT: A 285 GLU cc_start: 0.8251 (mp0) cc_final: 0.7770 (mp0) REVERT: A 287 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8788 (mm-30) REVERT: A 288 GLU cc_start: 0.8733 (tp30) cc_final: 0.8190 (tp30) REVERT: A 292 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8276 (mt-10) REVERT: A 377 HIS cc_start: 0.7622 (m-70) cc_final: 0.7306 (t70) REVERT: A 438 THR cc_start: 0.8961 (m) cc_final: 0.8567 (p) outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 0.1393 time to fit residues: 12.6486 Evaluate side-chains 67 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 374 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.0570 chunk 17 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.162253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128004 restraints weight = 4813.107| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.86 r_work: 0.3388 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3702 Z= 0.207 Angle : 0.633 8.326 5044 Z= 0.318 Chirality : 0.042 0.138 595 Planarity : 0.004 0.024 625 Dihedral : 4.343 22.220 504 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.85 % Favored : 95.94 % Rotamer: Outliers : 1.55 % Allowed : 26.36 % Favored : 72.09 % 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: 1.16 (0.40), residues: 468 helix: 1.23 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -0.82 (0.68), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 231 HIS 0.002 0.001 HIS A 97 PHE 0.016 0.002 PHE A 441 TYR 0.010 0.001 TYR A 258 ARG 0.001 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.373 Fit side-chains REVERT: A 93 TRP cc_start: 0.7717 (t-100) cc_final: 0.7500 (t-100) REVERT: A 285 GLU cc_start: 0.8183 (mp0) cc_final: 0.7766 (mp0) REVERT: A 287 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8730 (mm-30) REVERT: A 288 GLU cc_start: 0.8674 (tp30) cc_final: 0.8145 (tp30) REVERT: A 292 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8215 (mt-10) REVERT: A 377 HIS cc_start: 0.7567 (m-70) cc_final: 0.7144 (t70) REVERT: A 438 THR cc_start: 0.8923 (m) cc_final: 0.8541 (p) outliers start: 6 outliers final: 5 residues processed: 71 average time/residue: 0.1204 time to fit residues: 11.1886 Evaluate side-chains 70 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 366 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.159704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125596 restraints weight = 4859.767| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.84 r_work: 0.3356 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3702 Z= 0.250 Angle : 0.654 7.203 5044 Z= 0.330 Chirality : 0.043 0.142 595 Planarity : 0.004 0.024 625 Dihedral : 4.383 21.530 504 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.27 % Favored : 95.51 % Rotamer: Outliers : 2.07 % Allowed : 25.84 % Favored : 72.09 % 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: 1.33 (0.40), residues: 468 helix: 1.35 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -0.71 (0.67), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 315 HIS 0.002 0.000 HIS A 264 PHE 0.015 0.002 PHE A 117 TYR 0.010 0.001 TYR A 258 ARG 0.002 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.376 Fit side-chains REVERT: A 93 TRP cc_start: 0.7784 (t-100) cc_final: 0.7561 (t-100) REVERT: A 285 GLU cc_start: 0.8231 (mp0) cc_final: 0.7822 (mp0) REVERT: A 287 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8812 (mm-30) REVERT: A 288 GLU cc_start: 0.8779 (tp30) cc_final: 0.8221 (tp30) REVERT: A 292 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8287 (mt-10) REVERT: A 377 HIS cc_start: 0.7600 (m-70) cc_final: 0.7172 (t70) REVERT: A 438 THR cc_start: 0.8951 (m) cc_final: 0.8583 (p) outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.1271 time to fit residues: 11.5676 Evaluate side-chains 69 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 502 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 41 optimal weight: 0.8980 chunk 18 optimal weight: 0.0980 chunk 46 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.161534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127819 restraints weight = 4871.389| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.86 r_work: 0.3386 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3702 Z= 0.187 Angle : 0.630 7.192 5044 Z= 0.316 Chirality : 0.042 0.209 595 Planarity : 0.004 0.024 625 Dihedral : 4.312 21.360 504 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.06 % Favored : 95.73 % Rotamer: Outliers : 1.81 % Allowed : 25.84 % Favored : 72.35 % 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: 1.64 (0.41), residues: 468 helix: 1.57 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -0.70 (0.69), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 264 PHE 0.013 0.001 PHE A 208 TYR 0.010 0.001 TYR A 258 ARG 0.002 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 93 TRP cc_start: 0.7614 (t-100) cc_final: 0.7407 (t-100) REVERT: A 285 GLU cc_start: 0.8200 (mp0) cc_final: 0.7815 (mp0) REVERT: A 287 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8784 (mm-30) REVERT: A 288 GLU cc_start: 0.8733 (tp30) cc_final: 0.8182 (tp30) REVERT: A 292 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8201 (mt-10) REVERT: A 377 HIS cc_start: 0.7515 (m-70) cc_final: 0.7087 (t70) REVERT: A 438 THR cc_start: 0.8898 (m) cc_final: 0.8527 (p) outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 0.1287 time to fit residues: 11.4706 Evaluate side-chains 68 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 502 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.159643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125935 restraints weight = 4824.991| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.83 r_work: 0.3364 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3702 Z= 0.233 Angle : 0.652 7.686 5044 Z= 0.327 Chirality : 0.043 0.149 595 Planarity : 0.004 0.025 625 Dihedral : 4.321 21.125 504 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.49 % Favored : 95.30 % Rotamer: Outliers : 2.58 % Allowed : 24.55 % Favored : 72.87 % 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: 1.74 (0.41), residues: 468 helix: 1.63 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.60 (0.72), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 315 HIS 0.001 0.000 HIS A 264 PHE 0.014 0.002 PHE A 117 TYR 0.010 0.001 TYR A 258 ARG 0.001 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 93 TRP cc_start: 0.7710 (t-100) cc_final: 0.7509 (t-100) REVERT: A 285 GLU cc_start: 0.8228 (mp0) cc_final: 0.7855 (mp0) REVERT: A 287 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8806 (mm-30) REVERT: A 288 GLU cc_start: 0.8726 (tp30) cc_final: 0.8171 (tp30) REVERT: A 292 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8187 (mt-10) REVERT: A 377 HIS cc_start: 0.7590 (m-70) cc_final: 0.7184 (t70) REVERT: A 438 THR cc_start: 0.8926 (m) cc_final: 0.8556 (p) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.1172 time to fit residues: 11.1330 Evaluate side-chains 73 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 502 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.160320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126616 restraints weight = 4856.483| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.86 r_work: 0.3372 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3702 Z= 0.226 Angle : 0.656 8.537 5044 Z= 0.327 Chirality : 0.043 0.172 595 Planarity : 0.004 0.024 625 Dihedral : 4.308 20.534 504 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.27 % Favored : 95.51 % Rotamer: Outliers : 2.33 % Allowed : 25.84 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.78 (0.41), residues: 468 helix: 1.67 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.63 (0.70), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 231 HIS 0.001 0.000 HIS A 264 PHE 0.015 0.002 PHE A 208 TYR 0.011 0.001 TYR A 258 ARG 0.002 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.391 Fit side-chains REVERT: A 99 ARG cc_start: 0.7038 (mpp-170) cc_final: 0.6657 (mpp-170) REVERT: A 285 GLU cc_start: 0.8221 (mp0) cc_final: 0.7862 (mp0) REVERT: A 287 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8768 (mm-30) REVERT: A 288 GLU cc_start: 0.8706 (tp30) cc_final: 0.8155 (tp30) REVERT: A 292 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8145 (mt-10) REVERT: A 377 HIS cc_start: 0.7595 (m-70) cc_final: 0.7190 (t70) REVERT: A 438 THR cc_start: 0.8931 (m) cc_final: 0.8556 (p) outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.1184 time to fit residues: 11.5400 Evaluate side-chains 75 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 502 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.0170 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.160454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126953 restraints weight = 4830.361| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.83 r_work: 0.3375 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3702 Z= 0.223 Angle : 0.660 8.699 5044 Z= 0.328 Chirality : 0.044 0.185 595 Planarity : 0.004 0.024 625 Dihedral : 4.275 20.055 504 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.27 % Favored : 95.51 % Rotamer: Outliers : 2.07 % Allowed : 26.36 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.41), residues: 468 helix: 1.71 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -0.76 (0.70), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 264 PHE 0.014 0.002 PHE A 208 TYR 0.011 0.001 TYR A 258 ARG 0.001 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.414 Fit side-chains REVERT: A 99 ARG cc_start: 0.7147 (mpp-170) cc_final: 0.6743 (mpp-170) REVERT: A 260 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8121 (tt) REVERT: A 285 GLU cc_start: 0.8300 (mp0) cc_final: 0.7910 (mp0) REVERT: A 287 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8812 (mm-30) REVERT: A 288 GLU cc_start: 0.8742 (tp30) cc_final: 0.8156 (tp30) REVERT: A 292 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8182 (mt-10) REVERT: A 377 HIS cc_start: 0.7544 (m-70) cc_final: 0.7148 (t70) REVERT: A 438 THR cc_start: 0.8935 (m) cc_final: 0.8547 (p) outliers start: 8 outliers final: 6 residues processed: 73 average time/residue: 0.1254 time to fit residues: 12.0841 Evaluate side-chains 73 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 502 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 27 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 21 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.159833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126415 restraints weight = 4842.790| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.84 r_work: 0.3368 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3702 Z= 0.235 Angle : 0.669 8.922 5044 Z= 0.332 Chirality : 0.044 0.197 595 Planarity : 0.004 0.025 625 Dihedral : 4.270 19.937 504 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.06 % Favored : 95.73 % Rotamer: Outliers : 1.81 % Allowed : 26.61 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.41), residues: 468 helix: 1.70 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.67 (0.69), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 231 HIS 0.001 0.000 HIS A 264 PHE 0.013 0.002 PHE A 208 TYR 0.012 0.001 TYR A 258 ARG 0.002 0.000 ARG A 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 260 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8112 (tt) REVERT: A 285 GLU cc_start: 0.8357 (mp0) cc_final: 0.7954 (mp0) REVERT: A 287 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8834 (mm-30) REVERT: A 288 GLU cc_start: 0.8793 (tp30) cc_final: 0.8261 (tp30) REVERT: A 292 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8243 (mt-10) REVERT: A 377 HIS cc_start: 0.7518 (m-70) cc_final: 0.7141 (t70) REVERT: A 438 THR cc_start: 0.8941 (m) cc_final: 0.8553 (p) outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 0.1267 time to fit residues: 11.5168 Evaluate side-chains 73 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 502 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 35 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.159893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126469 restraints weight = 4877.911| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.84 r_work: 0.3370 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3702 Z= 0.234 Angle : 0.666 8.272 5044 Z= 0.331 Chirality : 0.044 0.181 595 Planarity : 0.004 0.025 625 Dihedral : 4.248 19.558 504 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.27 % Favored : 95.51 % Rotamer: Outliers : 1.55 % Allowed : 26.61 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.85 (0.41), residues: 468 helix: 1.72 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.67 (0.69), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 231 HIS 0.002 0.001 HIS A 264 PHE 0.013 0.002 PHE A 117 TYR 0.012 0.001 TYR A 258 ARG 0.001 0.000 ARG A 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2091.97 seconds wall clock time: 37 minutes 48.74 seconds (2268.74 seconds total)