Starting phenix.real_space_refine on Tue Feb 11 06:32:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n9y_0383/02_2025/6n9y_0383.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n9y_0383/02_2025/6n9y_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/cci-nas-00/data/ceres_data/6n9y_0383/02_2025/6n9y_0383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n9y_0383/02_2025/6n9y_0383.map" model { file = "/net/cci-nas-00/data/ceres_data/6n9y_0383/02_2025/6n9y_0383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n9y_0383/02_2025/6n9y_0383.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.13, per 1000 atoms: 0.69 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 - 3.00 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: 1.04 Conformation dependent library (CDL) restraints added in 521.1 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: 0.46 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: 1.17 Time building geometry restraints manager: 1.24 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: 0.00 - 1.86: 5743 1.86 - 3.72: 444 3.72 - 5.59: 54 5.59 - 7.45: 16 7.45 - 9.31: 5 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 3.040 nonbonded pdb=" O ALA A 452 " pdb=" OG SER A 455 " model vdw 2.268 3.040 nonbonded pdb=" OD2 ASP A 77 " pdb=" OG1 THR A 80 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR A 168 " pdb=" OD1 ASN A 238 " model vdw 2.358 3.040 nonbonded pdb=" O MET A 52 " pdb=" OG1 THR A 56 " model vdw 2.363 3.040 ... (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: 1.850 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 14.110 Find NCS groups from input model: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.880 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.514 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: 0.2692 time to fit residues: 35.7918 Evaluate side-chains 60 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 49 optimal weight: 0.0270 overall best weight: 3.0044 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.071250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.063599 restraints weight = 17865.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.065336 restraints weight = 9365.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.066536 restraints weight = 5835.693| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4636 Z= 0.192 Angle : 0.671 7.980 6262 Z= 0.356 Chirality : 0.043 0.188 653 Planarity : 0.005 0.054 812 Dihedral : 6.177 34.387 628 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.88 % Allowed : 9.38 % 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: -3.20 (0.31), residues: 550 helix: -2.29 (0.25), residues: 267 sheet: -1.10 (0.99), residues: 29 loop : -1.93 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 326 HIS 0.004 0.001 HIS A 276 PHE 0.014 0.001 PHE A 272 TYR 0.016 0.001 TYR A 169 ARG 0.006 0.001 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 84 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7271 (m-80) REVERT: A 50 ARG cc_start: 0.7676 (ttm110) cc_final: 0.7445 (ptp-170) REVERT: A 70 LEU cc_start: 0.9282 (tp) cc_final: 0.8889 (tp) REVERT: A 246 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8251 (mp10) REVERT: A 534 GLU cc_start: 0.7870 (tp30) cc_final: 0.7522 (pm20) REVERT: A 535 SER cc_start: 0.8751 (t) cc_final: 0.8068 (p) REVERT: A 549 ARG cc_start: 0.6573 (ttm110) cc_final: 0.5989 (ttt180) outliers start: 9 outliers final: 4 residues processed: 82 average time/residue: 0.2053 time to fit residues: 20.7505 Evaluate side-chains 66 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 48 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 33 optimal weight: 40.0000 chunk 25 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.069715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.062054 restraints weight = 18266.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.063766 restraints weight = 9554.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.064931 restraints weight = 6010.389| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4636 Z= 0.201 Angle : 0.617 6.784 6262 Z= 0.323 Chirality : 0.042 0.165 653 Planarity : 0.004 0.039 812 Dihedral : 5.654 31.929 626 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 1.46 % Allowed : 12.08 % Favored : 86.46 % 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: -2.08 (0.35), residues: 550 helix: -1.16 (0.29), residues: 263 sheet: -1.13 (0.97), residues: 29 loop : -1.55 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.008 0.001 HIS A 320 PHE 0.015 0.002 PHE A 272 TYR 0.014 0.002 TYR A 253 ARG 0.004 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 to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.533 Fit side-chains REVERT: A 39 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7139 (m-80) REVERT: A 66 ARG cc_start: 0.8316 (tpm170) cc_final: 0.8113 (tpm170) REVERT: A 230 MET cc_start: 0.7963 (mtm) cc_final: 0.7752 (mpp) REVERT: A 510 MET cc_start: 0.7919 (mmm) cc_final: 0.7713 (mmt) REVERT: A 534 GLU cc_start: 0.7711 (tp30) cc_final: 0.7224 (pm20) REVERT: A 535 SER cc_start: 0.8720 (t) cc_final: 0.7987 (p) outliers start: 7 outliers final: 4 residues processed: 70 average time/residue: 0.2017 time to fit residues: 17.8458 Evaluate side-chains 58 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 495 LEU 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 24 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 37 optimal weight: 40.0000 chunk 52 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3196 r_free = 0.3196 target = 0.069882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.062005 restraints weight = 18187.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.063733 restraints weight = 9532.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.064932 restraints weight = 5999.425| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4016 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= 0.208 Angle : 0.596 6.809 6262 Z= 0.312 Chirality : 0.041 0.157 653 Planarity : 0.004 0.035 812 Dihedral : 5.442 29.158 626 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.67 % Allowed : 14.38 % Favored : 83.96 % 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: -1.66 (0.36), residues: 550 helix: -0.75 (0.31), residues: 267 sheet: -0.72 (1.03), residues: 29 loop : -1.45 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 326 HIS 0.003 0.001 HIS A 276 PHE 0.014 0.001 PHE A 272 TYR 0.012 0.001 TYR A 169 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 66 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7070 (m-80) REVERT: A 66 ARG cc_start: 0.8386 (tpm170) cc_final: 0.8122 (tpm170) REVERT: A 70 LEU cc_start: 0.9167 (tp) cc_final: 0.8605 (mt) REVERT: A 230 MET cc_start: 0.7980 (mtm) cc_final: 0.7728 (mpp) outliers start: 8 outliers final: 5 residues processed: 64 average time/residue: 0.1674 time to fit residues: 13.9401 Evaluate side-chains 56 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 276 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 8 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.069766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.061758 restraints weight = 18532.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.063508 restraints weight = 9777.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.064702 restraints weight = 6139.130| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4210 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= 0.206 Angle : 0.602 6.814 6262 Z= 0.313 Chirality : 0.041 0.154 653 Planarity : 0.004 0.035 812 Dihedral : 5.305 27.998 626 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.71 % Allowed : 15.00 % Favored : 82.29 % 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: -1.46 (0.36), residues: 550 helix: -0.54 (0.31), residues: 269 sheet: -0.77 (1.01), residues: 29 loop : -1.40 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 326 HIS 0.002 0.001 HIS A 276 PHE 0.013 0.001 PHE A 272 TYR 0.013 0.001 TYR A 169 ARG 0.002 0.000 ARG A 281 *********************** 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 66 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: A 230 MET cc_start: 0.7998 (mtm) cc_final: 0.7728 (mpp) outliers start: 13 outliers final: 6 residues processed: 61 average time/residue: 0.1686 time to fit residues: 13.4013 Evaluate side-chains 57 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 495 LEU 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 1 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 49 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 13 optimal weight: 0.0980 chunk 53 optimal weight: 6.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- 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 = 0.3206 r_free = 0.3206 target = 0.070465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.062574 restraints weight = 18022.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.064331 restraints weight = 9377.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.065552 restraints weight = 5850.226| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4422 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= 0.165 Angle : 0.581 6.762 6262 Z= 0.300 Chirality : 0.041 0.150 653 Planarity : 0.004 0.038 812 Dihedral : 5.055 25.832 626 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.29 % Allowed : 16.25 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.36), residues: 550 helix: -0.35 (0.31), residues: 270 sheet: -0.70 (1.01), residues: 29 loop : -1.41 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 326 HIS 0.004 0.001 HIS A 276 PHE 0.010 0.001 PHE A 272 TYR 0.013 0.001 TYR A 169 ARG 0.003 0.000 ARG A 200 *********************** 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 71 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7480 (m-80) REVERT: A 68 VAL cc_start: 0.7975 (t) cc_final: 0.7689 (p) REVERT: A 230 MET cc_start: 0.7968 (mtm) cc_final: 0.7495 (mpp) outliers start: 11 outliers final: 7 residues processed: 67 average time/residue: 0.1587 time to fit residues: 14.0595 Evaluate side-chains 62 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE 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 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 38 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 34 optimal weight: 0.0570 chunk 19 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- 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 = 0.3209 r_free = 0.3209 target = 0.070598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.062833 restraints weight = 17885.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.064565 restraints weight = 9263.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.065760 restraints weight = 5757.629| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4636 Z= 0.186 Angle : 0.597 7.562 6262 Z= 0.310 Chirality : 0.041 0.144 653 Planarity : 0.004 0.037 812 Dihedral : 4.986 25.567 626 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 2.08 % Allowed : 17.08 % Favored : 80.83 % 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: -1.17 (0.36), residues: 550 helix: -0.21 (0.31), residues: 270 sheet: -0.79 (0.97), residues: 29 loop : -1.33 (0.42), residues: 251 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 0.014 0.001 TYR A 248 ARG 0.002 0.000 ARG A 281 *********************** 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 63 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: A 230 MET cc_start: 0.8053 (mtm) cc_final: 0.7454 (mpp) REVERT: A 501 GLU cc_start: 0.6933 (tp30) cc_final: 0.6716 (tp30) REVERT: A 510 MET cc_start: 0.8201 (mmt) cc_final: 0.7912 (mmt) outliers start: 10 outliers final: 9 residues processed: 58 average time/residue: 0.1565 time to fit residues: 12.2001 Evaluate side-chains 60 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE 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 401 THR 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 31 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 53 optimal weight: 40.0000 chunk 3 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3203 r_free = 0.3203 target = 0.070335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.062639 restraints weight = 18048.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.064334 restraints weight = 9349.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.065519 restraints weight = 5826.878| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4611 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= 0.189 Angle : 0.592 6.677 6262 Z= 0.307 Chirality : 0.041 0.144 653 Planarity : 0.004 0.038 812 Dihedral : 4.950 23.914 626 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.50 % Allowed : 17.29 % Favored : 80.21 % 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: -1.04 (0.37), residues: 550 helix: -0.13 (0.31), residues: 270 sheet: -0.63 (0.99), residues: 29 loop : -1.26 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 326 HIS 0.003 0.001 HIS A 236 PHE 0.008 0.001 PHE A 272 TYR 0.025 0.001 TYR A 248 ARG 0.002 0.000 ARG A 281 *********************** 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 65 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: A 52 MET cc_start: 0.8127 (ttt) cc_final: 0.7901 (tpp) REVERT: A 230 MET cc_start: 0.7980 (mtm) cc_final: 0.7473 (mpp) REVERT: A 510 MET cc_start: 0.8200 (mmt) cc_final: 0.7922 (mmt) outliers start: 12 outliers final: 10 residues processed: 60 average time/residue: 0.1595 time to fit residues: 12.8258 Evaluate side-chains 59 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE 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 362 THR Chi-restraints excluded: chain A residue 401 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 20 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3202 r_free = 0.3202 target = 0.070286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.062504 restraints weight = 18120.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.064201 restraints weight = 9462.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.065382 restraints weight = 5919.615| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4654 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= 0.199 Angle : 0.607 6.698 6262 Z= 0.314 Chirality : 0.041 0.152 653 Planarity : 0.004 0.037 812 Dihedral : 5.004 26.612 626 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 2.50 % Allowed : 17.71 % 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: -1.04 (0.37), residues: 550 helix: -0.13 (0.31), residues: 270 sheet: -0.52 (0.99), residues: 29 loop : -1.27 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 326 HIS 0.003 0.001 HIS A 236 PHE 0.015 0.001 PHE A 272 TYR 0.022 0.001 TYR A 248 ARG 0.002 0.000 ARG A 66 *********************** 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 63 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: A 52 MET cc_start: 0.8171 (ttt) cc_final: 0.7904 (tpp) REVERT: A 230 MET cc_start: 0.7992 (mtm) cc_final: 0.7550 (mpp) REVERT: A 510 MET cc_start: 0.8219 (mmt) cc_final: 0.7921 (mmt) outliers start: 12 outliers final: 10 residues processed: 57 average time/residue: 0.1451 time to fit residues: 11.3554 Evaluate side-chains 60 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 362 THR Chi-restraints excluded: chain A residue 401 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3198 r_free = 0.3198 target = 0.070058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.062317 restraints weight = 18146.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.064018 restraints weight = 9522.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.065213 restraints weight = 5960.515| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4710 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= 0.207 Angle : 0.618 6.647 6262 Z= 0.319 Chirality : 0.042 0.151 653 Planarity : 0.004 0.037 812 Dihedral : 5.052 25.578 626 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 2.29 % Allowed : 18.96 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.37), residues: 550 helix: -0.16 (0.31), residues: 270 sheet: -0.44 (0.99), residues: 29 loop : -1.29 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 326 HIS 0.003 0.001 HIS A 236 PHE 0.018 0.001 PHE A 272 TYR 0.022 0.001 TYR A 248 ARG 0.003 0.000 ARG A 66 ********************** 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 64 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: A 52 MET cc_start: 0.8295 (ttt) cc_final: 0.7988 (tpp) REVERT: A 66 ARG cc_start: 0.8399 (tpm170) cc_final: 0.8054 (tpm170) REVERT: A 230 MET cc_start: 0.8098 (mtm) cc_final: 0.7536 (mpp) REVERT: A 281 ARG cc_start: 0.8031 (ptm-80) cc_final: 0.7247 (ptm-80) REVERT: A 510 MET cc_start: 0.8247 (mmt) cc_final: 0.7921 (mmt) outliers start: 11 outliers final: 10 residues processed: 60 average time/residue: 0.1806 time to fit residues: 14.0440 Evaluate side-chains 61 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 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 401 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 0.0570 chunk 26 optimal weight: 0.3980 chunk 39 optimal weight: 10.0000 overall best weight: 2.8904 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.070648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.062708 restraints weight = 18125.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.064396 restraints weight = 9595.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.065568 restraints weight = 6083.276| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4876 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= 0.168 Angle : 0.614 7.574 6262 Z= 0.309 Chirality : 0.041 0.148 653 Planarity : 0.004 0.037 812 Dihedral : 4.827 24.576 626 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.29 % Allowed : 18.75 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.37), residues: 550 helix: -0.01 (0.32), residues: 270 sheet: -0.40 (0.98), residues: 29 loop : -1.18 (0.43), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 326 HIS 0.003 0.001 HIS A 236 PHE 0.016 0.001 PHE A 272 TYR 0.020 0.001 TYR A 248 ARG 0.002 0.000 ARG A 281 =============================================================================== Job complete usr+sys time: 1449.09 seconds wall clock time: 26 minutes 54.59 seconds (1614.59 seconds total)