Starting phenix.real_space_refine on Thu Dec 7 20:45:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/12_2023/6n9y_0383.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/12_2023/6n9y_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_0383/12_2023/6n9y_0383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/12_2023/6n9y_0383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/12_2023/6n9y_0383.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/12_2023/6n9y_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-1.21rc1-5172/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: 2.97, per 1000 atoms: 0.66 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: 1.94 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.17 Time building geometry restraints manager: 2.09 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: 0.360 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: 1.920 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.420 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.790 ------------------------------------------------------------------------------- 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 : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 107 average time/residue: 0.2439 time to fit residues: 31.0371 Evaluate side-chains 58 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.530 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7336 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4636 Z= 0.203 Angle : 0.655 7.802 6262 Z= 0.351 Chirality : 0.042 0.175 653 Planarity : 0.005 0.057 812 Dihedral : 6.183 35.252 626 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.45 % Favored : 92.36 % Rotamer: Outliers : 2.71 % Allowed : 8.96 % Favored : 88.33 % 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: -3.09 (0.32), residues: 550 helix: -2.24 (0.25), residues: 261 sheet: -1.10 (1.00), residues: 29 loop : -1.83 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 326 HIS 0.007 0.001 HIS A 276 PHE 0.016 0.002 PHE A 272 TYR 0.011 0.002 TYR A 330 ARG 0.005 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 85 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.602 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 80 average time/residue: 0.2069 time to fit residues: 20.9436 Evaluate side-chains 56 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.565 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0487 time to fit residues: 1.2594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 13 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 17 optimal weight: 0.0970 chunk 40 optimal weight: 20.0000 overall best weight: 4.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3774 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= 0.181 Angle : 0.599 5.989 6262 Z= 0.313 Chirality : 0.041 0.171 653 Planarity : 0.004 0.042 812 Dihedral : 5.666 33.862 626 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 1.25 % Allowed : 13.54 % 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: -2.14 (0.34), residues: 550 helix: -1.17 (0.29), residues: 266 sheet: -0.81 (1.01), residues: 29 loop : -1.68 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 326 HIS 0.006 0.001 HIS A 320 PHE 0.012 0.001 PHE A 272 TYR 0.015 0.001 TYR A 253 ARG 0.003 0.000 ARG A 281 *********************** 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 66 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.535 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 65 average time/residue: 0.1703 time to fit residues: 14.5328 Evaluate side-chains 53 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.572 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0580 time to fit residues: 0.9390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 5 optimal weight: 40.0000 chunk 23 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4068 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= 0.197 Angle : 0.571 5.016 6262 Z= 0.300 Chirality : 0.041 0.155 653 Planarity : 0.004 0.036 812 Dihedral : 5.428 30.317 626 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.67 % Allowed : 13.96 % Favored : 84.38 % 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: -1.75 (0.35), residues: 550 helix: -0.76 (0.30), residues: 271 sheet: -0.44 (1.05), residues: 29 loop : -1.63 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 326 HIS 0.004 0.001 HIS A 276 PHE 0.011 0.001 PHE A 272 TYR 0.011 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 64 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.551 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 0.1582 time to fit residues: 12.8790 Evaluate side-chains 57 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0468 time to fit residues: 1.1959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4636 Z= 0.262 Angle : 0.621 5.541 6262 Z= 0.324 Chirality : 0.042 0.153 653 Planarity : 0.004 0.034 812 Dihedral : 5.576 28.943 626 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 1.88 % Allowed : 15.62 % Favored : 82.50 % 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: -1.56 (0.35), residues: 550 helix: -0.58 (0.31), residues: 265 sheet: -0.34 (1.07), residues: 29 loop : -1.55 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 326 HIS 0.005 0.001 HIS A 276 PHE 0.011 0.002 PHE A 272 TYR 0.012 0.002 TYR A 14 ARG 0.004 0.000 ARG A 423 *********************** 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 61 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 58 average time/residue: 0.1482 time to fit residues: 11.7254 Evaluate side-chains 53 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.577 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0516 time to fit residues: 0.9753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 13 optimal weight: 0.0570 chunk 53 optimal weight: 0.1980 chunk 44 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- 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: 0.7314 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4636 Z= 0.141 Angle : 0.587 9.676 6262 Z= 0.295 Chirality : 0.040 0.152 653 Planarity : 0.004 0.035 812 Dihedral : 5.079 29.650 626 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 1.25 % Allowed : 16.67 % Favored : 82.08 % 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: -1.05 (0.36), residues: 550 helix: -0.15 (0.32), residues: 263 sheet: -0.12 (1.08), residues: 29 loop : -1.29 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 326 HIS 0.003 0.001 HIS A 276 PHE 0.007 0.001 PHE A 272 TYR 0.011 0.001 TYR A 169 ARG 0.003 0.000 ARG A 281 *********************** 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 73 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 0.1720 time to fit residues: 15.3347 Evaluate side-chains 55 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.527 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0607 time to fit residues: 1.1374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 38 optimal weight: 40.0000 chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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: 0.7434 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4636 Z= 0.274 Angle : 0.659 8.448 6262 Z= 0.336 Chirality : 0.043 0.148 653 Planarity : 0.005 0.037 812 Dihedral : 5.438 28.618 626 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 1.88 % Allowed : 17.29 % 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: -1.24 (0.36), residues: 550 helix: -0.28 (0.32), residues: 264 sheet: -0.97 (0.87), residues: 39 loop : -1.31 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 326 HIS 0.003 0.001 HIS A 398 PHE 0.013 0.002 PHE A 170 TYR 0.013 0.002 TYR A 14 ARG 0.004 0.001 ARG A 66 *********************** 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 62 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 58 average time/residue: 0.1530 time to fit residues: 11.9069 Evaluate side-chains 59 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.561 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0482 time to fit residues: 1.3772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 0.0970 chunk 4 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 overall best weight: 3.1784 ------------------------------------------------------------------------------- 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: 0.7364 moved from start: 0.4808 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= 0.169 Angle : 0.602 8.312 6262 Z= 0.304 Chirality : 0.040 0.151 653 Planarity : 0.004 0.036 812 Dihedral : 5.146 29.201 626 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.21 % Allowed : 18.33 % 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: -0.92 (0.37), residues: 550 helix: -0.07 (0.32), residues: 263 sheet: -0.01 (1.04), residues: 29 loop : -1.20 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 326 HIS 0.003 0.001 HIS A 236 PHE 0.009 0.001 PHE A 4 TYR 0.013 0.001 TYR A 169 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 57 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.1714 time to fit residues: 12.7357 Evaluate side-chains 53 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 0.0170 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 52 optimal weight: 0.0970 chunk 31 optimal weight: 0.0570 overall best weight: 1.6336 ------------------------------------------------------------------------------- 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: 0.7306 moved from start: 0.5051 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= 0.147 Angle : 0.573 6.370 6262 Z= 0.289 Chirality : 0.040 0.146 653 Planarity : 0.004 0.034 812 Dihedral : 4.787 26.997 626 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.21 % Allowed : 18.75 % 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: -0.73 (0.37), residues: 550 helix: 0.09 (0.33), residues: 264 sheet: 0.17 (1.06), residues: 29 loop : -1.11 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 326 HIS 0.003 0.001 HIS A 344 PHE 0.007 0.001 PHE A 4 TYR 0.012 0.001 TYR A 169 ARG 0.003 0.000 ARG A 281 *********************** 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 62 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.1751 time to fit residues: 13.9654 Evaluate side-chains 53 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.531 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0803 time to fit residues: 0.9174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 33 optimal weight: 40.0000 chunk 26 optimal weight: 0.0470 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 13 optimal weight: 0.0370 overall best weight: 2.4160 ------------------------------------------------------------------------------- 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: 0.7316 moved from start: 0.5126 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= 0.161 Angle : 0.614 10.486 6262 Z= 0.307 Chirality : 0.040 0.140 653 Planarity : 0.004 0.034 812 Dihedral : 4.835 27.542 626 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.21 % Allowed : 19.58 % 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: -0.79 (0.37), residues: 550 helix: 0.04 (0.33), residues: 264 sheet: 0.12 (1.03), residues: 29 loop : -1.14 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 326 HIS 0.003 0.001 HIS A 236 PHE 0.039 0.001 PHE A 272 TYR 0.025 0.001 TYR A 248 ARG 0.009 0.000 ARG A 281 ********************** 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 58 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 57 average time/residue: 0.1926 time to fit residues: 13.9329 Evaluate side-chains 55 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.505 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0446 time to fit residues: 0.7923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 12 optimal weight: 0.0870 chunk 43 optimal weight: 0.4980 chunk 18 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 overall best weight: 3.9164 ------------------------------------------------------------------------------- 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 = 0.3241 r_free = 0.3241 target = 0.072478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.064504 restraints weight = 18316.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.066268 restraints weight = 9742.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.067471 restraints weight = 6179.171| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.5118 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= 0.182 Angle : 0.607 8.002 6262 Z= 0.309 Chirality : 0.041 0.140 653 Planarity : 0.004 0.034 812 Dihedral : 4.907 27.306 626 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % 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: -0.84 (0.37), residues: 550 helix: 0.01 (0.32), residues: 266 sheet: 0.18 (1.05), residues: 29 loop : -1.20 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A 326 HIS 0.003 0.001 HIS A 236 PHE 0.021 0.001 PHE A 272 TYR 0.024 0.001 TYR A 248 ARG 0.004 0.000 ARG A 281 =============================================================================== Job complete usr+sys time: 1108.32 seconds wall clock time: 20 minutes 54.70 seconds (1254.70 seconds total)