Starting phenix.real_space_refine on Sun Mar 10 19:52:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/03_2024/6n9y_0383.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/03_2024/6n9y_0383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/03_2024/6n9y_0383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/03_2024/6n9y_0383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/03_2024/6n9y_0383.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/03_2024/6n9y_0383.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.009 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 39 5.16 5 C 2874 2.51 5 N 798 2.21 5 O 816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4527 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4527 Classifications: {'peptide': 552} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 531} Time building chain proxies: 2.89, per 1000 atoms: 0.64 Number of scatterers: 4527 At special positions: 0 Unit cell: (104.86, 72.76, 112.35, 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 39 16.00 O 816 8.00 N 798 7.00 C 2874 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 - 3.50 Amino acid : False - 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: 1.83 Conformation dependent library (CDL) restraints added in 863.2 milliseconds 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1040 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 4 sheets defined 56.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 3.990A pdb=" N TYR A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 25 removed outlier: 4.098A pdb=" N ALA A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ALA A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 38 removed outlier: 4.239A pdb=" N CYS A 37 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 38 " --> pdb=" O ARG A 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 34 through 38' Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 60 through 73 removed outlier: 4.204A pdb=" N TYR A 65 " --> pdb=" O PRO A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 91 removed outlier: 4.235A pdb=" N GLN A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 115 removed outlier: 3.638A pdb=" N LYS A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.613A pdb=" N VAL A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.812A pdb=" N ILE A 145 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 146 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 202 removed outlier: 4.325A pdb=" N GLY A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 194 " --> pdb=" O GLN A 190 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 195 " --> pdb=" O HIS A 191 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A 200 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 230 through 249 removed outlier: 3.545A pdb=" N ALA A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS A 235 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.619A pdb=" N TRP A 307 " --> pdb=" O TRP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 318 removed outlier: 3.533A pdb=" N GLU A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.776A pdb=" N ILE A 328 " --> pdb=" O TRP A 324 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.982A pdb=" N LEU A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.927A pdb=" N LEU A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 removed outlier: 3.760A pdb=" N ILE A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 414 " --> pdb=" O ALA A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.626A pdb=" N PHE A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 443 " --> pdb=" O MET A 439 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP A 447 " --> pdb=" O VAL A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 465 removed outlier: 3.553A pdb=" N ARG A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 491 removed outlier: 4.115A pdb=" N ASP A 487 " --> pdb=" O GLY A 483 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 491 " --> pdb=" O ASP A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 519 removed outlier: 3.757A pdb=" N GLU A 501 " --> pdb=" O GLU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 550 removed outlier: 4.065A pdb=" N LEU A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 149 Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 162 removed outlier: 3.699A pdb=" N PHE A 159 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 161 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ALA A 167 " --> pdb=" O MET A 218 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 220 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR A 169 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 354 removed outlier: 3.638A pdb=" N CYS A 351 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 353 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 368 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR A 369 " --> pdb=" O ASN A 403 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ASN A 403 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 399 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS A 398 " --> pdb=" O ILE A 395 " (cutoff:3.500A) 166 hydrogen bonds defined for protein. 483 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: 1.28 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1485 1.34 - 1.46: 1065 1.46 - 1.58: 2025 1.58 - 1.70: 0 1.70 - 1.82: 61 Bond restraints: 4636 Sorted by residual: bond pdb=" N ARG A 164 " pdb=" CA ARG A 164 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.17e-02 7.31e+03 7.73e+00 bond pdb=" C SER A 365 " pdb=" N PRO A 366 " ideal model delta sigma weight residual 1.336 1.314 0.022 1.25e-02 6.40e+03 3.17e+00 bond pdb=" CA ALA A 126 " pdb=" C ALA A 126 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.94e+00 bond pdb=" C GLU A 60 " pdb=" O GLU A 60 " ideal model delta sigma weight residual 1.249 1.237 0.011 8.50e-03 1.38e+04 1.80e+00 bond pdb=" N ASN A 40 " pdb=" CA ASN A 40 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.66e+00 ... (remaining 4631 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.87: 90 105.87 - 112.94: 2365 112.94 - 120.01: 1780 120.01 - 127.08: 1966 127.08 - 134.15: 61 Bond angle restraints: 6262 Sorted by residual: angle pdb=" N GLY A 363 " pdb=" CA GLY A 363 " pdb=" C GLY A 363 " ideal model delta sigma weight residual 112.33 118.30 -5.97 1.10e+00 8.26e-01 2.95e+01 angle pdb=" C THR A 204 " pdb=" N CYS A 205 " pdb=" CA CYS A 205 " ideal model delta sigma weight residual 120.51 128.35 -7.84 1.45e+00 4.76e-01 2.92e+01 angle pdb=" C TYR A 163 " pdb=" N ARG A 164 " pdb=" CA ARG A 164 " ideal model delta sigma weight residual 121.19 128.46 -7.27 1.59e+00 3.96e-01 2.09e+01 angle pdb=" C THR A 362 " pdb=" N GLY A 363 " pdb=" CA GLY A 363 " ideal model delta sigma weight residual 120.44 124.68 -4.24 1.09e+00 8.42e-01 1.51e+01 angle pdb=" N ALA A 126 " pdb=" CA ALA A 126 " pdb=" C ALA A 126 " ideal model delta sigma weight residual 110.91 106.37 4.54 1.17e+00 7.31e-01 1.51e+01 ... (remaining 6257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.03: 2355 10.03 - 20.06: 321 20.06 - 30.09: 68 30.09 - 40.12: 23 40.12 - 50.16: 13 Dihedral angle restraints: 2780 sinusoidal: 1161 harmonic: 1619 Sorted by residual: dihedral pdb=" CA ASN A 129 " pdb=" C ASN A 129 " pdb=" N SER A 130 " pdb=" CA SER A 130 " ideal model delta harmonic sigma weight residual -180.00 -138.60 -41.40 0 5.00e+00 4.00e-02 6.86e+01 dihedral pdb=" CA GLU A 255 " pdb=" C GLU A 255 " pdb=" N GLU A 256 " pdb=" CA GLU A 256 " ideal model delta harmonic sigma weight residual -180.00 -146.08 -33.92 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA THR A 406 " pdb=" C THR A 406 " pdb=" N GLY A 407 " pdb=" CA GLY A 407 " ideal model delta harmonic sigma weight residual -180.00 -147.03 -32.97 0 5.00e+00 4.00e-02 4.35e+01 ... (remaining 2777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 383 0.043 - 0.086: 203 0.086 - 0.129: 49 0.129 - 0.171: 16 0.171 - 0.214: 2 Chirality restraints: 653 Sorted by residual: chirality pdb=" CB ILE A 313 " pdb=" CA ILE A 313 " pdb=" CG1 ILE A 313 " pdb=" CG2 ILE A 313 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE A 166 " pdb=" CA ILE A 166 " pdb=" CG1 ILE A 166 " pdb=" CG2 ILE A 166 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CG LEU A 135 " pdb=" CB LEU A 135 " pdb=" CD1 LEU A 135 " pdb=" CD2 LEU A 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 650 not shown) Planarity restraints: 812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 530 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.46e+00 pdb=" N PRO A 531 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 531 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 531 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 25 " 0.042 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO A 26 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 142 " -0.040 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO A 143 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 143 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 143 " -0.034 5.00e-02 4.00e+02 ... (remaining 809 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 892 2.76 - 3.30: 4207 3.30 - 3.83: 7008 3.83 - 4.37: 8154 4.37 - 4.90: 13831 Nonbonded interactions: 34092 Sorted by model distance: nonbonded pdb=" O VAL A 155 " pdb=" OH TYR A 169 " model vdw 2.229 2.440 nonbonded pdb=" O ALA A 452 " pdb=" OG SER A 455 " model vdw 2.268 2.440 nonbonded pdb=" OD2 ASP A 77 " pdb=" OG1 THR A 80 " model vdw 2.311 2.440 nonbonded pdb=" OH TYR A 168 " pdb=" OD1 ASN A 238 " model vdw 2.358 2.440 nonbonded pdb=" O MET A 52 " pdb=" OG1 THR A 56 " model vdw 2.363 2.440 ... (remaining 34087 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 group one per residue 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: 0.340 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: 1.960 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.000 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 0.008 0.063 4636 Z= 0.493 Angle : 1.101 9.311 6262 Z= 0.644 Chirality : 0.054 0.214 653 Planarity : 0.007 0.064 812 Dihedral : 10.299 50.156 1740 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.42 % Allowed : 1.04 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: -4.98 (0.27), residues: 550 helix: -4.16 (0.15), residues: 249 sheet: -2.11 (0.73), residues: 51 loop : -2.47 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 433 HIS 0.015 0.003 HIS A 398 PHE 0.023 0.003 PHE A 485 TYR 0.026 0.003 TYR A 253 ARG 0.009 0.001 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 ILE cc_start: 0.8735 (tp) cc_final: 0.8527 (mt) REVERT: A 449 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7410 (pp) REVERT: A 510 MET cc_start: 0.7131 (mmm) cc_final: 0.6854 (mmm) outliers start: 2 outliers final: 0 residues processed: 107 average time/residue: 0.2430 time to fit residues: 30.8640 Evaluate side-chains 60 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 124 GLN A 236 HIS A 276 HIS A 338 GLN A 347 GLN A 391 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4636 Z= 0.205 Angle : 0.657 7.661 6262 Z= 0.352 Chirality : 0.043 0.179 653 Planarity : 0.005 0.057 812 Dihedral : 6.318 35.226 628 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.45 % Favored : 92.36 % Rotamer: Outliers : 2.71 % Allowed : 8.54 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.10 (0.31), residues: 550 helix: -2.25 (0.25), residues: 257 sheet: -1.08 (1.00), residues: 29 loop : -1.86 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 326 HIS 0.003 0.001 HIS A 276 PHE 0.015 0.002 PHE A 272 TYR 0.010 0.002 TYR A 93 ARG 0.003 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.557 Fit side-chains REVERT: A 39 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.6742 (m-80) REVERT: A 240 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.5892 (m-80) REVERT: A 510 MET cc_start: 0.7466 (mmm) cc_final: 0.7190 (mmm) REVERT: A 535 SER cc_start: 0.7897 (OUTLIER) cc_final: 0.7244 (p) REVERT: A 549 ARG cc_start: 0.6875 (ttm110) cc_final: 0.6138 (ttt180) outliers start: 13 outliers final: 5 residues processed: 81 average time/residue: 0.2029 time to fit residues: 20.3763 Evaluate side-chains 59 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 535 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 13 optimal weight: 0.0370 chunk 50 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 44 optimal weight: 0.4980 chunk 49 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 overall best weight: 4.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4636 Z= 0.196 Angle : 0.609 6.153 6262 Z= 0.318 Chirality : 0.041 0.165 653 Planarity : 0.004 0.042 812 Dihedral : 5.749 33.621 626 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.92 % Allowed : 11.88 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.31 (0.34), residues: 550 helix: -1.31 (0.29), residues: 270 sheet: -0.91 (0.99), residues: 29 loop : -1.76 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 326 HIS 0.007 0.001 HIS A 320 PHE 0.013 0.001 PHE A 272 TYR 0.015 0.002 TYR A 253 ARG 0.003 0.000 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.534 Fit side-chains REVERT: A 39 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.6728 (m-80) REVERT: A 240 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.6077 (m-80) REVERT: A 549 ARG cc_start: 0.6933 (ttm110) cc_final: 0.6159 (ttt180) outliers start: 14 outliers final: 8 residues processed: 68 average time/residue: 0.1760 time to fit residues: 15.3052 Evaluate side-chains 60 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 548 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 26 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4636 Z= 0.192 Angle : 0.577 5.015 6262 Z= 0.303 Chirality : 0.041 0.156 653 Planarity : 0.004 0.037 812 Dihedral : 5.498 31.158 626 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.50 % Allowed : 12.71 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.35), residues: 550 helix: -0.79 (0.30), residues: 271 sheet: -0.45 (1.05), residues: 29 loop : -1.63 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 326 HIS 0.003 0.001 HIS A 276 PHE 0.011 0.001 PHE A 272 TYR 0.012 0.001 TYR A 14 ARG 0.002 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6668 (m-80) REVERT: A 70 LEU cc_start: 0.8757 (tp) cc_final: 0.8213 (mt) REVERT: A 230 MET cc_start: 0.7009 (mpp) cc_final: 0.6359 (mtm) REVERT: A 240 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.6189 (m-80) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.1854 time to fit residues: 15.3768 Evaluate side-chains 60 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 548 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 0.0570 chunk 47 optimal weight: 20.0000 chunk 13 optimal weight: 0.1980 chunk 17 optimal weight: 20.0000 overall best weight: 3.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4636 Z= 0.175 Angle : 0.565 6.356 6262 Z= 0.293 Chirality : 0.040 0.151 653 Planarity : 0.004 0.036 812 Dihedral : 5.201 30.059 626 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 3.54 % Allowed : 14.17 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.36), residues: 550 helix: -0.39 (0.31), residues: 269 sheet: -0.29 (1.06), residues: 29 loop : -1.44 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 326 HIS 0.003 0.001 HIS A 276 PHE 0.009 0.001 PHE A 272 TYR 0.011 0.001 TYR A 169 ARG 0.002 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6743 (m-80) REVERT: A 70 LEU cc_start: 0.8818 (tp) cc_final: 0.8363 (mt) REVERT: A 145 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.8026 (pt) REVERT: A 230 MET cc_start: 0.7108 (mpp) cc_final: 0.6552 (mtm) REVERT: A 240 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6154 (m-80) outliers start: 17 outliers final: 9 residues processed: 71 average time/residue: 0.1558 time to fit residues: 14.5395 Evaluate side-chains 64 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 548 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 0.0050 chunk 44 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 30.0000 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4636 Z= 0.183 Angle : 0.582 7.161 6262 Z= 0.301 Chirality : 0.041 0.151 653 Planarity : 0.004 0.034 812 Dihedral : 5.152 29.565 626 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.92 % Allowed : 16.04 % Favored : 81.04 % 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: -1.23 (0.36), residues: 550 helix: -0.24 (0.31), residues: 271 sheet: -0.29 (1.02), residues: 29 loop : -1.47 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 326 HIS 0.003 0.001 HIS A 320 PHE 0.009 0.001 PHE A 272 TYR 0.012 0.001 TYR A 169 ARG 0.002 0.000 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.7014 (m-80) REVERT: A 145 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.8023 (pt) REVERT: A 230 MET cc_start: 0.7104 (mpp) cc_final: 0.6610 (mtm) REVERT: A 240 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.6245 (m-80) outliers start: 14 outliers final: 9 residues processed: 65 average time/residue: 0.1499 time to fit residues: 13.0678 Evaluate side-chains 63 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 548 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4636 Z= 0.183 Angle : 0.579 7.131 6262 Z= 0.297 Chirality : 0.041 0.152 653 Planarity : 0.004 0.033 812 Dihedral : 5.019 29.380 626 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 2.92 % Allowed : 15.83 % Favored : 81.25 % 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 (0.37), residues: 550 helix: -0.08 (0.32), residues: 268 sheet: -0.09 (1.03), residues: 29 loop : -1.30 (0.42), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 326 HIS 0.002 0.001 HIS A 335 PHE 0.007 0.001 PHE A 272 TYR 0.012 0.001 TYR A 169 ARG 0.002 0.000 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6963 (m-80) REVERT: A 145 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7992 (pt) REVERT: A 230 MET cc_start: 0.7001 (mpp) cc_final: 0.6517 (mtm) REVERT: A 240 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6187 (m-80) outliers start: 14 outliers final: 11 residues processed: 60 average time/residue: 0.1461 time to fit residues: 11.9589 Evaluate side-chains 64 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 548 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.1980 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 48 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4636 Z= 0.194 Angle : 0.582 6.927 6262 Z= 0.300 Chirality : 0.041 0.144 653 Planarity : 0.004 0.033 812 Dihedral : 5.038 29.226 626 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 3.12 % Allowed : 16.46 % Favored : 80.42 % 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 (0.37), residues: 550 helix: -0.10 (0.32), residues: 270 sheet: 0.11 (1.05), residues: 29 loop : -1.28 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 326 HIS 0.002 0.001 HIS A 398 PHE 0.008 0.001 PHE A 4 TYR 0.013 0.001 TYR A 169 ARG 0.003 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 53 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6889 (m-80) REVERT: A 230 MET cc_start: 0.6987 (mpp) cc_final: 0.6541 (mtm) REVERT: A 240 TYR cc_start: 0.7363 (OUTLIER) cc_final: 0.6244 (m-80) outliers start: 15 outliers final: 12 residues processed: 62 average time/residue: 0.1586 time to fit residues: 13.0034 Evaluate side-chains 65 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 548 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 52 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4636 Z= 0.160 Angle : 0.581 6.852 6262 Z= 0.293 Chirality : 0.040 0.142 653 Planarity : 0.004 0.033 812 Dihedral : 4.830 28.999 626 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.12 % Allowed : 16.46 % Favored : 80.42 % 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: -0.83 (0.37), residues: 550 helix: -0.05 (0.32), residues: 268 sheet: 0.18 (1.04), residues: 29 loop : -1.11 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 326 HIS 0.003 0.001 HIS A 276 PHE 0.011 0.001 PHE A 382 TYR 0.012 0.001 TYR A 169 ARG 0.003 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.6791 (m-80) REVERT: A 230 MET cc_start: 0.6908 (mpp) cc_final: 0.6374 (mtm) outliers start: 15 outliers final: 12 residues processed: 68 average time/residue: 0.1522 time to fit residues: 13.7513 Evaluate side-chains 64 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 548 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 54 optimal weight: 0.0670 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 33 optimal weight: 40.0000 chunk 26 optimal weight: 20.0000 chunk 34 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4636 Z= 0.186 Angle : 0.607 7.014 6262 Z= 0.307 Chirality : 0.041 0.140 653 Planarity : 0.004 0.033 812 Dihedral : 4.890 28.692 626 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.71 % Allowed : 17.50 % Favored : 79.79 % 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: -0.75 (0.37), residues: 550 helix: -0.06 (0.32), residues: 266 sheet: 0.31 (1.06), residues: 29 loop : -0.98 (0.43), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 326 HIS 0.003 0.001 HIS A 398 PHE 0.008 0.001 PHE A 272 TYR 0.012 0.001 TYR A 169 ARG 0.006 0.000 ARG A 323 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6741 (m-80) REVERT: A 230 MET cc_start: 0.6891 (mpp) cc_final: 0.6453 (mtm) outliers start: 13 outliers final: 12 residues processed: 60 average time/residue: 0.1468 time to fit residues: 11.9117 Evaluate side-chains 63 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 548 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3201 r_free = 0.3201 target = 0.070679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.062921 restraints weight = 18492.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.064652 restraints weight = 9700.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.065839 restraints weight = 6073.668| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4636 Z= 0.189 Angle : 0.627 10.417 6262 Z= 0.311 Chirality : 0.041 0.141 653 Planarity : 0.004 0.033 812 Dihedral : 4.901 28.577 626 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.33 % Allowed : 17.29 % Favored : 79.38 % 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: -0.83 (0.37), residues: 550 helix: -0.11 (0.32), residues: 268 sheet: 0.38 (1.05), residues: 29 loop : -1.07 (0.42), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 326 HIS 0.002 0.001 HIS A 344 PHE 0.011 0.001 PHE A 4 TYR 0.012 0.001 TYR A 169 ARG 0.003 0.000 ARG A 103 =============================================================================== Job complete usr+sys time: 1102.38 seconds wall clock time: 20 minutes 48.41 seconds (1248.41 seconds total)