Starting phenix.real_space_refine on Fri Aug 22 14:51:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n9y_0383/08_2025/6n9y_0383.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n9y_0383/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/6n9y_0383/08_2025/6n9y_0383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n9y_0383/08_2025/6n9y_0383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n9y_0383/08_2025/6n9y_0383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n9y_0383/08_2025/6n9y_0383.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.29, per 1000 atoms: 0.28 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: 0.25 Conformation dependent library (CDL) restraints added in 107.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.15 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: 0.69 Time building geometry restraints manager: 0.36 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: 0.010 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.000 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.300 ------------------------------------------------------------------------------- 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= 0.355 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG A 423 TYR 0.026 0.003 TYR A 253 PHE 0.023 0.003 PHE A 485 TRP 0.015 0.003 TRP A 433 HIS 0.015 0.003 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00766 ( 4636) covalent geometry : angle 1.10123 ( 6262) hydrogen bonds : bond 0.31800 ( 166) hydrogen bonds : angle 10.51166 ( 483) *********************** 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 : 0.188 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: 0.0892 time to fit residues: 11.3321 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 : 0.151 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 = 0.3194 r_free = 0.3194 target = 0.070651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.063103 restraints weight = 18008.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.064810 restraints weight = 9345.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.065991 restraints weight = 5811.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.066857 restraints weight = 4006.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.067445 restraints weight = 2943.948| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4636 Z= 0.153 Angle : 0.674 7.764 6262 Z= 0.360 Chirality : 0.043 0.179 653 Planarity : 0.006 0.055 812 Dihedral : 6.259 34.408 628 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.08 % Allowed : 8.96 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.24 (0.31), residues: 550 helix: -2.33 (0.25), residues: 267 sheet: -1.15 (0.99), residues: 29 loop : -1.94 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 66 TYR 0.015 0.002 TYR A 169 PHE 0.016 0.002 PHE A 272 TRP 0.010 0.001 TRP A 326 HIS 0.005 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4636) covalent geometry : angle 0.67421 ( 6262) hydrogen bonds : bond 0.05038 ( 166) hydrogen bonds : angle 5.62268 ( 483) *********************** 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 82 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.177 Fit side-chains REVERT: A 39 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7233 (m-80) REVERT: A 70 LEU cc_start: 0.9298 (tp) cc_final: 0.8830 (tp) REVERT: A 246 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8259 (mp10) REVERT: A 534 GLU cc_start: 0.7770 (tp30) cc_final: 0.7481 (pm20) REVERT: A 535 SER cc_start: 0.8776 (t) cc_final: 0.8120 (p) REVERT: A 549 ARG cc_start: 0.6583 (ttm110) cc_final: 0.5994 (ttt180) outliers start: 10 outliers final: 4 residues processed: 80 average time/residue: 0.0675 time to fit residues: 6.7782 Evaluate side-chains 63 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 4 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 0.0770 chunk 2 optimal weight: 0.0670 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 overall best weight: 4.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** 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 = 0.3193 r_free = 0.3193 target = 0.069918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.062121 restraints weight = 18211.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.063853 restraints weight = 9553.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.065030 restraints weight = 5993.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.065877 restraints weight = 4184.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.066482 restraints weight = 3128.533| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3673 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= 0.133 Angle : 0.614 6.811 6262 Z= 0.321 Chirality : 0.042 0.165 653 Planarity : 0.004 0.039 812 Dihedral : 5.654 31.903 626 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.35), residues: 550 helix: -1.17 (0.30), residues: 262 sheet: -1.03 (0.97), residues: 29 loop : -1.53 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.015 0.002 TYR A 253 PHE 0.015 0.002 PHE A 272 TRP 0.007 0.001 TRP A 326 HIS 0.007 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4636) covalent geometry : angle 0.61370 ( 6262) hydrogen bonds : bond 0.03983 ( 166) hydrogen bonds : angle 5.19574 ( 483) *********************** 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 71 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.186 Fit side-chains REVERT: A 39 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: A 101 MET cc_start: 0.8499 (mtp) cc_final: 0.8175 (mtt) REVERT: A 510 MET cc_start: 0.7907 (mmm) cc_final: 0.7606 (mmt) REVERT: A 534 GLU cc_start: 0.7667 (tp30) cc_final: 0.7204 (pm20) REVERT: A 535 SER cc_start: 0.8705 (t) cc_final: 0.7969 (p) outliers start: 7 outliers final: 4 residues processed: 69 average time/residue: 0.0692 time to fit residues: 6.2625 Evaluate side-chains 61 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 19 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 11 optimal weight: 30.0000 chunk 37 optimal weight: 40.0000 chunk 42 optimal weight: 9.9990 chunk 13 optimal weight: 0.0070 chunk 25 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 overall best weight: 5.0006 ------------------------------------------------------------------------------- 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 = 0.3197 r_free = 0.3197 target = 0.070058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.062015 restraints weight = 18166.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.063754 restraints weight = 9695.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.064980 restraints weight = 6127.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.065818 restraints weight = 4285.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.066456 restraints weight = 3219.988| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4033 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= 0.137 Angle : 0.597 6.913 6262 Z= 0.311 Chirality : 0.041 0.157 653 Planarity : 0.004 0.035 812 Dihedral : 5.466 29.148 626 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.08 % Allowed : 13.33 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.36), residues: 550 helix: -0.74 (0.31), residues: 267 sheet: -0.77 (1.02), residues: 29 loop : -1.45 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 297 TYR 0.012 0.001 TYR A 169 PHE 0.015 0.001 PHE A 272 TRP 0.009 0.001 TRP A 326 HIS 0.002 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4636) covalent geometry : angle 0.59723 ( 6262) hydrogen bonds : bond 0.03597 ( 166) hydrogen bonds : angle 5.01813 ( 483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7068 (m-80) REVERT: A 66 ARG cc_start: 0.8401 (tpm170) cc_final: 0.8109 (tpm170) REVERT: A 70 LEU cc_start: 0.9201 (tp) cc_final: 0.8694 (mt) REVERT: A 510 MET cc_start: 0.7915 (mmm) cc_final: 0.7708 (mmt) outliers start: 10 outliers final: 5 residues processed: 67 average time/residue: 0.0563 time to fit residues: 4.9616 Evaluate side-chains 57 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 12 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 = 0.3167 r_free = 0.3167 target = 0.068835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.060928 restraints weight = 18465.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.062644 restraints weight = 9836.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.063817 restraints weight = 6238.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.064653 restraints weight = 4382.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.065272 restraints weight = 3289.822| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4636 Z= 0.185 Angle : 0.652 6.872 6262 Z= 0.339 Chirality : 0.043 0.156 653 Planarity : 0.005 0.035 812 Dihedral : 5.565 28.189 626 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.71 % Allowed : 16.04 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.36), residues: 550 helix: -0.63 (0.31), residues: 269 sheet: -1.56 (0.81), residues: 39 loop : -1.43 (0.43), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.013 0.002 TYR A 14 PHE 0.013 0.002 PHE A 272 TRP 0.007 0.001 TRP A 326 HIS 0.003 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 4636) covalent geometry : angle 0.65185 ( 6262) hydrogen bonds : bond 0.03749 ( 166) hydrogen bonds : angle 5.14012 ( 483) *********************** 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 64 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7353 (m-80) outliers start: 13 outliers final: 7 residues processed: 59 average time/residue: 0.0601 time to fit residues: 4.7892 Evaluate side-chains 57 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 498 ASP Chi-restraints excluded: chain A residue 548 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 0.0170 chunk 6 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 20.0000 overall best weight: 3.5624 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.070017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.062054 restraints weight = 18312.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.063796 restraints weight = 9665.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.064977 restraints weight = 6067.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.065805 restraints weight = 4243.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.066347 restraints weight = 3184.526| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4393 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= 0.116 Angle : 0.582 6.860 6262 Z= 0.301 Chirality : 0.041 0.155 653 Planarity : 0.004 0.039 812 Dihedral : 5.121 25.442 626 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 1.67 % Allowed : 16.46 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.36), residues: 550 helix: -0.37 (0.31), residues: 268 sheet: -0.77 (1.02), residues: 29 loop : -1.45 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.012 0.001 TYR A 169 PHE 0.009 0.001 PHE A 272 TRP 0.006 0.001 TRP A 326 HIS 0.002 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4636) covalent geometry : angle 0.58199 ( 6262) hydrogen bonds : bond 0.03189 ( 166) hydrogen bonds : angle 4.80211 ( 483) *********************** 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 65 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7478 (m-80) REVERT: A 68 VAL cc_start: 0.7882 (t) cc_final: 0.7629 (p) REVERT: A 331 MET cc_start: 0.8636 (ppp) cc_final: 0.8435 (ppp) REVERT: A 510 MET cc_start: 0.8248 (mmt) cc_final: 0.7810 (mmt) outliers start: 8 outliers final: 5 residues processed: 63 average time/residue: 0.0576 time to fit residues: 4.8570 Evaluate side-chains 57 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 276 HIS Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 495 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 0.0000 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 53 optimal weight: 40.0000 chunk 52 optimal weight: 8.9990 overall best weight: 4.7590 ------------------------------------------------------------------------------- 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 = 0.3189 r_free = 0.3189 target = 0.069660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.061830 restraints weight = 18180.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.063523 restraints weight = 9587.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.064680 restraints weight = 6028.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.065357 restraints weight = 4231.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.066019 restraints weight = 3293.249| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4636 Z= 0.137 Angle : 0.609 8.457 6262 Z= 0.315 Chirality : 0.041 0.146 653 Planarity : 0.004 0.040 812 Dihedral : 5.092 25.292 626 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 2.29 % Allowed : 16.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.36), residues: 550 helix: -0.20 (0.32), residues: 269 sheet: -0.77 (1.00), residues: 29 loop : -1.45 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 323 TYR 0.012 0.001 TYR A 169 PHE 0.009 0.001 PHE A 170 TRP 0.038 0.001 TRP A 326 HIS 0.003 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4636) covalent geometry : angle 0.60928 ( 6262) hydrogen bonds : bond 0.03317 ( 166) hydrogen bonds : angle 4.84265 ( 483) *********************** 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 to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: A 68 VAL cc_start: 0.7835 (t) cc_final: 0.7601 (p) REVERT: A 510 MET cc_start: 0.8272 (mmt) cc_final: 0.8026 (mmt) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.0417 time to fit residues: 3.3735 Evaluate side-chains 61 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 49 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 30 optimal weight: 40.0000 chunk 1 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3170 r_free = 0.3170 target = 0.068840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.061016 restraints weight = 18470.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.062677 restraints weight = 9729.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.063834 restraints weight = 6140.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.064616 restraints weight = 4323.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.065232 restraints weight = 3292.634| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4636 Z= 0.169 Angle : 0.642 7.725 6262 Z= 0.332 Chirality : 0.043 0.147 653 Planarity : 0.004 0.038 812 Dihedral : 5.296 24.883 626 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.50 % Allowed : 16.88 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.37), residues: 550 helix: -0.19 (0.32), residues: 266 sheet: -1.39 (0.79), residues: 39 loop : -1.25 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.013 0.001 TYR A 14 PHE 0.011 0.001 PHE A 170 TRP 0.023 0.001 TRP A 326 HIS 0.003 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 4636) covalent geometry : angle 0.64204 ( 6262) hydrogen bonds : bond 0.03487 ( 166) hydrogen bonds : angle 4.94808 ( 483) *********************** 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 62 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7494 (m-80) REVERT: A 510 MET cc_start: 0.8290 (mmt) cc_final: 0.8027 (mmt) outliers start: 12 outliers final: 10 residues processed: 57 average time/residue: 0.0526 time to fit residues: 4.0743 Evaluate side-chains 58 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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 34 optimal weight: 0.2980 chunk 11 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 47 optimal weight: 0.0170 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 16 optimal weight: 30.0000 chunk 42 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.6624 ------------------------------------------------------------------------------- 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 = 0.3213 r_free = 0.3213 target = 0.070778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.062800 restraints weight = 18162.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.064513 restraints weight = 9590.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.065715 restraints weight = 6072.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.066511 restraints weight = 4260.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.067087 restraints weight = 3211.772| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4742 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= 0.113 Angle : 0.601 7.279 6262 Z= 0.309 Chirality : 0.041 0.154 653 Planarity : 0.004 0.034 812 Dihedral : 4.927 24.501 626 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 2.08 % Allowed : 17.50 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.37), residues: 550 helix: -0.07 (0.33), residues: 266 sheet: -0.42 (0.98), residues: 29 loop : -1.17 (0.43), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.013 0.001 TYR A 169 PHE 0.008 0.001 PHE A 272 TRP 0.020 0.001 TRP A 326 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 4636) covalent geometry : angle 0.60135 ( 6262) hydrogen bonds : bond 0.03050 ( 166) hydrogen bonds : angle 4.69877 ( 483) *********************** 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 70 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7475 (m-80) REVERT: A 175 LEU cc_start: 0.7799 (tt) cc_final: 0.7508 (tp) REVERT: A 281 ARG cc_start: 0.7929 (ptm-80) cc_final: 0.7297 (ptm-80) REVERT: A 510 MET cc_start: 0.8219 (mmt) cc_final: 0.7988 (mmt) outliers start: 10 outliers final: 8 residues processed: 65 average time/residue: 0.0657 time to fit residues: 5.3846 Evaluate side-chains 61 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 chunk 40 optimal weight: 30.0000 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.069442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.061691 restraints weight = 18209.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.063346 restraints weight = 9595.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.064522 restraints weight = 6048.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.065322 restraints weight = 4239.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.065912 restraints weight = 3177.250| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4636 Z= 0.168 Angle : 0.672 7.344 6262 Z= 0.344 Chirality : 0.044 0.155 653 Planarity : 0.004 0.037 812 Dihedral : 5.216 24.846 626 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 1.88 % Allowed : 18.96 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.37), residues: 550 helix: -0.15 (0.32), residues: 268 sheet: -1.17 (0.81), residues: 39 loop : -1.30 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.016 0.001 TYR A 248 PHE 0.018 0.002 PHE A 272 TRP 0.050 0.002 TRP A 326 HIS 0.003 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 4636) covalent geometry : angle 0.67250 ( 6262) hydrogen bonds : bond 0.03405 ( 166) hydrogen bonds : angle 4.86997 ( 483) ********************** 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: 9 poor density : 55 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: A 175 LEU cc_start: 0.8122 (tt) cc_final: 0.7891 (tp) REVERT: A 281 ARG cc_start: 0.7977 (ptm-80) cc_final: 0.7114 (ptm-80) REVERT: A 510 MET cc_start: 0.8293 (mmt) cc_final: 0.8027 (mmt) outliers start: 9 outliers final: 7 residues processed: 59 average time/residue: 0.0519 time to fit residues: 4.1589 Evaluate side-chains 61 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 509 GLU Chi-restraints excluded: chain A residue 548 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.2651 > 50: distance: 26 - 46: 6.926 distance: 41 - 46: 7.290 distance: 46 - 47: 8.370 distance: 47 - 48: 12.670 distance: 47 - 50: 15.676 distance: 48 - 49: 22.283 distance: 48 - 54: 18.497 distance: 50 - 51: 20.573 distance: 51 - 52: 8.433 distance: 51 - 53: 25.793 distance: 54 - 55: 32.735 distance: 55 - 56: 30.247 distance: 55 - 58: 20.662 distance: 56 - 57: 36.157 distance: 56 - 63: 15.884 distance: 58 - 59: 19.047 distance: 59 - 60: 14.328 distance: 60 - 61: 15.912 distance: 61 - 62: 26.610 distance: 63 - 64: 21.488 distance: 64 - 65: 31.110 distance: 65 - 66: 43.663 distance: 65 - 67: 26.508 distance: 67 - 68: 26.746 distance: 67 - 73: 16.500 distance: 68 - 69: 21.284 distance: 68 - 71: 21.927 distance: 69 - 70: 25.382 distance: 69 - 74: 22.189 distance: 71 - 72: 13.481 distance: 72 - 73: 19.602 distance: 74 - 75: 16.913 distance: 75 - 76: 17.479 distance: 75 - 78: 15.809 distance: 76 - 77: 38.278 distance: 76 - 83: 16.056 distance: 78 - 79: 13.762 distance: 79 - 80: 21.337 distance: 80 - 81: 26.700 distance: 80 - 82: 21.510 distance: 83 - 84: 10.091 distance: 84 - 87: 48.668 distance: 85 - 86: 25.722 distance: 85 - 91: 26.675 distance: 87 - 88: 20.676 distance: 88 - 89: 18.601 distance: 88 - 90: 30.976 distance: 91 - 92: 31.369 distance: 92 - 93: 24.421 distance: 92 - 95: 18.820 distance: 93 - 94: 15.711 distance: 93 - 97: 38.607 distance: 94 - 123: 34.155 distance: 95 - 96: 31.095 distance: 97 - 98: 3.075 distance: 98 - 99: 12.274 distance: 98 - 101: 11.710 distance: 99 - 100: 23.825 distance: 99 - 106: 9.069 distance: 101 - 102: 5.679 distance: 102 - 103: 16.244 distance: 103 - 104: 4.929 distance: 103 - 105: 14.895 distance: 106 - 107: 22.285 distance: 107 - 108: 4.796 distance: 107 - 110: 21.323 distance: 108 - 109: 16.595 distance: 108 - 114: 12.153 distance: 109 - 139: 22.086 distance: 110 - 111: 9.939 distance: 111 - 112: 9.074 distance: 111 - 113: 17.483 distance: 114 - 115: 21.165 distance: 115 - 116: 26.106 distance: 115 - 118: 8.881 distance: 116 - 117: 17.619 distance: 116 - 123: 17.459 distance: 117 - 145: 26.899 distance: 118 - 119: 23.507 distance: 119 - 120: 23.301 distance: 120 - 121: 13.333 distance: 120 - 122: 38.371