Starting phenix.real_space_refine on Tue Aug 4 19:13:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x5f_66586/08_2026/9x5f_66586.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x5f_66586/08_2026/9x5f_66586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x5f_66586/08_2026/9x5f_66586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x5f_66586/08_2026/9x5f_66586.map" model { file = "/net/cci-nas-00/data/ceres_data/9x5f_66586/08_2026/9x5f_66586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x5f_66586/08_2026/9x5f_66586.cif" } resolution = 3.11 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.028 sd= 0.432 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 28 5.16 5 C 3908 2.51 5 N 1050 2.21 5 O 1135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6121 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2720 Classifications: {'peptide': 337} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 321} Chain: "A" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3376 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 16, 'TRANS': 417} Chain breaks: 2 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'GA3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.44, per 1000 atoms: 0.24 Number of scatterers: 6121 At special positions: 0 Unit cell: (73.6, 82.8, 103.96, 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 28 16.00 O 1135 8.00 N 1050 7.00 C 3908 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: 0.46 Conformation dependent library (CDL) restraints added in 354.7 milliseconds 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 3 sheets defined 51.5% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'B' and resid 17 through 32 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.722A pdb=" N GLU B 97 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 193 through 207 Processing helix chain 'B' and resid 230 through 236 Processing helix chain 'B' and resid 243 through 255 removed outlier: 3.547A pdb=" N ARG B 247 " --> pdb=" O ARG B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 332 through 347 removed outlier: 3.720A pdb=" N TYR B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.679A pdb=" N LEU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 93 removed outlier: 3.655A pdb=" N GLY A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER A 92 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.596A pdb=" N ILE A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 209 through 228 removed outlier: 3.561A pdb=" N VAL A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 246 removed outlier: 3.714A pdb=" N SER A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 250 through 268 removed outlier: 3.515A pdb=" N LYS A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 291 removed outlier: 4.145A pdb=" N SER A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 309 Processing helix chain 'A' and resid 327 through 338 removed outlier: 3.589A pdb=" N LEU A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 376 Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.619A pdb=" N ASP A 391 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.884A pdb=" N ALA A 418 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 Processing helix chain 'A' and resid 451 through 472 removed outlier: 3.513A pdb=" N LEU A 466 " --> pdb=" O TYR A 462 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY A 472 " --> pdb=" O ASP A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'A' and resid 512 through 516 removed outlier: 4.034A pdb=" N ASP A 515 " --> pdb=" O GLU A 512 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 516 " --> pdb=" O GLY A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 512 through 516' Processing helix chain 'A' and resid 522 through 534 Processing helix chain 'A' and resid 542 through 555 Processing sheet with id=AA1, first strand: chain 'B' and resid 314 through 319 removed outlier: 6.453A pdb=" N SER B 286 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU B 317 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 288 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU B 319 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 290 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN B 217 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N CYS B 289 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B 219 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ALA B 291 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL B 185 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE B 218 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N MET B 187 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU B 220 " --> pdb=" O MET B 187 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLY B 189 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL B 108 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ALA B 188 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL B 110 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 145 " --> pdb=" O PHE B 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 385 removed outlier: 6.339A pdb=" N PHE A 345 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ARG A 382 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 347 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE A 384 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLY A 349 " --> pdb=" O PHE A 384 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL A 315 " --> pdb=" O ARG A 346 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR A 348 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL A 317 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE A 350 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP A 319 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 437 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA A 584 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 385 removed outlier: 6.339A pdb=" N PHE A 345 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ARG A 382 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 347 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE A 384 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLY A 349 " --> pdb=" O PHE A 384 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL A 315 " --> pdb=" O ARG A 346 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR A 348 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL A 317 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE A 350 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP A 319 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 437 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 572 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 581 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 570 " --> pdb=" O ALA A 581 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 930 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: 0.71 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1072 1.32 - 1.44: 1653 1.44 - 1.56: 3495 1.56 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 6266 Sorted by residual: bond pdb=" N GLN B 90 " pdb=" CA GLN B 90 " ideal model delta sigma weight residual 1.459 1.489 -0.030 9.10e-03 1.21e+04 1.09e+01 bond pdb=" N VAL A 385 " pdb=" CA VAL A 385 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.27e-02 6.20e+03 7.57e+00 bond pdb=" N ASP B 95 " pdb=" CA ASP B 95 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.33e-02 5.65e+03 6.45e+00 bond pdb=" N TRP B 174 " pdb=" CA TRP B 174 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.33e-02 5.65e+03 6.43e+00 bond pdb=" N MET A 120 " pdb=" CA MET A 120 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.18e+00 ... (remaining 6261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 8195 1.19 - 2.37: 230 2.37 - 3.56: 62 3.56 - 4.75: 9 4.75 - 5.93: 5 Bond angle restraints: 8501 Sorted by residual: angle pdb=" N ASP B 95 " pdb=" CA ASP B 95 " pdb=" C ASP B 95 " ideal model delta sigma weight residual 113.28 109.25 4.03 1.22e+00 6.72e-01 1.09e+01 angle pdb=" C TRP B 91 " pdb=" CA TRP B 91 " pdb=" CB TRP B 91 " ideal model delta sigma weight residual 110.67 116.60 -5.93 1.92e+00 2.71e-01 9.55e+00 angle pdb=" CA ASP B 95 " pdb=" CB ASP B 95 " pdb=" CG ASP B 95 " ideal model delta sigma weight residual 112.60 115.39 -2.79 1.00e+00 1.00e+00 7.77e+00 angle pdb=" N PHE A 279 " pdb=" CA PHE A 279 " pdb=" C PHE A 279 " ideal model delta sigma weight residual 111.28 108.33 2.95 1.09e+00 8.42e-01 7.31e+00 angle pdb=" CA LYS B 182 " pdb=" C LYS B 182 " pdb=" O LYS B 182 " ideal model delta sigma weight residual 121.60 118.55 3.05 1.21e+00 6.83e-01 6.34e+00 ... (remaining 8496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.18: 3337 13.18 - 26.35: 352 26.35 - 39.53: 79 39.53 - 52.71: 14 52.71 - 65.88: 2 Dihedral angle restraints: 3784 sinusoidal: 1558 harmonic: 2226 Sorted by residual: dihedral pdb=" CA GLY B 92 " pdb=" C GLY B 92 " pdb=" N VAL B 93 " pdb=" CA VAL B 93 " ideal model delta harmonic sigma weight residual 180.00 160.47 19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ASP A 75 " pdb=" C ASP A 75 " pdb=" N MET A 76 " pdb=" CA MET A 76 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA VAL A 509 " pdb=" C VAL A 509 " pdb=" N ALA A 510 " pdb=" CA ALA A 510 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 3781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 713 0.041 - 0.082: 147 0.082 - 0.124: 63 0.124 - 0.165: 6 0.165 - 0.206: 2 Chirality restraints: 931 Sorted by residual: chirality pdb=" CA TRP B 91 " pdb=" N TRP B 91 " pdb=" C TRP B 91 " pdb=" CB TRP B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA VAL A 385 " pdb=" N VAL A 385 " pdb=" C VAL A 385 " pdb=" CB VAL A 385 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.73e-01 ... (remaining 928 not shown) Planarity restraints: 1097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 264 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.22e+00 pdb=" C ALA A 264 " 0.031 2.00e-02 2.50e+03 pdb=" O ALA A 264 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG A 265 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 155 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO B 156 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 156 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 156 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 413 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C LEU A 413 " 0.025 2.00e-02 2.50e+03 pdb=" O LEU A 413 " -0.009 2.00e-02 2.50e+03 pdb=" N HIS A 414 " -0.008 2.00e-02 2.50e+03 ... (remaining 1094 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 656 2.75 - 3.29: 6023 3.29 - 3.82: 10061 3.82 - 4.36: 11192 4.36 - 4.90: 19796 Nonbonded interactions: 47728 Sorted by model distance: nonbonded pdb=" O ALA A 355 " pdb=" OG1 THR A 358 " model vdw 2.211 3.040 nonbonded pdb=" O PHE B 241 " pdb=" O13 GA3 B 401 " model vdw 2.222 3.040 nonbonded pdb=" ND2 ASN A 448 " pdb=" OE2 GLU A 521 " model vdw 2.278 3.120 nonbonded pdb=" OE2 GLU B 274 " pdb=" NZ LYS B 275 " model vdw 2.281 3.120 nonbonded pdb=" OH TYR B 21 " pdb=" OE2 GLU A 84 " model vdw 2.282 3.040 ... (remaining 47723 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.650 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 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 : 0.003 0.035 6266 Z= 0.170 Angle : 0.511 5.933 8501 Z= 0.289 Chirality : 0.042 0.206 931 Planarity : 0.004 0.039 1097 Dihedral : 11.199 65.884 2352 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: 0.56 (0.30), residues: 763 helix: 1.56 (0.27), residues: 359 sheet: 0.79 (0.48), residues: 103 loop : -1.27 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 43 TYR 0.012 0.001 TYR A 500 PHE 0.011 0.001 PHE B 155 TRP 0.014 0.002 TRP B 91 HIS 0.003 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.17 ( 6266) covalent geometry : angle 0.51140 / 0.29 ( 8501) hydrogen bonds : bond 0.16054 / 10.20 ( 304) hydrogen bonds : angle 5.67905 / 3.98 ( 930) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8721 (ptp-110) cc_final: 0.8515 (mtm110) REVERT: B 104 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7908 (tm-30) REVERT: A 314 ARG cc_start: 0.7759 (tpp80) cc_final: 0.7215 (mtm-85) REVERT: A 357 ASN cc_start: 0.8561 (t0) cc_final: 0.8208 (m-40) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0951 time to fit residues: 16.3361 Evaluate side-chains 95 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.0170 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 ASN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 HIS A 428 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.068279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.059835 restraints weight = 17708.695| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.60 r_work: 0.2940 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6266 Z= 0.126 Angle : 0.554 7.525 8501 Z= 0.287 Chirality : 0.041 0.170 931 Planarity : 0.004 0.039 1097 Dihedral : 4.896 21.292 915 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.99 % Allowed : 13.02 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: 1.03 (0.31), residues: 763 helix: 1.88 (0.27), residues: 367 sheet: 0.94 (0.49), residues: 110 loop : -1.04 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 253 TYR 0.012 0.001 TYR A 500 PHE 0.014 0.001 PHE A 411 TRP 0.009 0.001 TRP A 328 HIS 0.003 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 6266) covalent geometry : angle 0.55377 / 0.29 ( 8501) hydrogen bonds : bond 0.04543 / 2.80 ( 304) hydrogen bonds : angle 4.20520 / 2.93 ( 930) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8722 (ptp-110) cc_final: 0.8512 (mtm110) REVERT: B 104 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7964 (tm-30) REVERT: A 266 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.6389 (tpp-160) REVERT: A 314 ARG cc_start: 0.7742 (tpp80) cc_final: 0.7165 (mtm-85) REVERT: A 354 GLN cc_start: 0.8044 (pp30) cc_final: 0.7650 (tt0) REVERT: A 530 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.6908 (mpt) outliers start: 13 outliers final: 6 residues processed: 114 average time/residue: 0.0974 time to fit residues: 13.9696 Evaluate side-chains 109 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 530 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 71 optimal weight: 0.0030 chunk 51 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN A 209 GLN ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.059587 restraints weight = 17529.043| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.58 r_work: 0.2939 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6266 Z= 0.115 Angle : 0.528 6.657 8501 Z= 0.271 Chirality : 0.041 0.145 931 Planarity : 0.004 0.037 1097 Dihedral : 4.546 17.146 915 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.45 % Allowed : 15.47 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: 1.11 (0.30), residues: 763 helix: 1.92 (0.27), residues: 367 sheet: 1.09 (0.49), residues: 110 loop : -1.01 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 71 TYR 0.011 0.001 TYR B 240 PHE 0.012 0.001 PHE B 155 TRP 0.008 0.001 TRP A 328 HIS 0.003 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 6266) covalent geometry : angle 0.52799 / 0.27 ( 8501) hydrogen bonds : bond 0.04051 / 2.46 ( 304) hydrogen bonds : angle 3.94776 / 2.76 ( 930) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8776 (ptp-110) cc_final: 0.8553 (mtm110) REVERT: B 104 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7950 (tm-30) REVERT: A 88 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7517 (tmm) REVERT: A 220 MET cc_start: 0.8344 (mmt) cc_final: 0.7431 (mmt) REVERT: A 266 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.6152 (tpp-160) REVERT: A 314 ARG cc_start: 0.7838 (tpp80) cc_final: 0.7231 (mtm-85) REVERT: A 530 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.6781 (mpt) outliers start: 16 outliers final: 4 residues processed: 110 average time/residue: 0.0866 time to fit residues: 11.9994 Evaluate side-chains 100 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 530 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 0.0970 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.067224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.058818 restraints weight = 17697.803| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.59 r_work: 0.2917 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6266 Z= 0.125 Angle : 0.531 6.812 8501 Z= 0.273 Chirality : 0.041 0.135 931 Planarity : 0.004 0.036 1097 Dihedral : 4.423 15.754 915 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.68 % Allowed : 16.39 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: 1.09 (0.31), residues: 763 helix: 1.90 (0.27), residues: 367 sheet: 1.07 (0.50), residues: 110 loop : -1.02 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 71 TYR 0.011 0.001 TYR A 500 PHE 0.015 0.001 PHE B 76 TRP 0.009 0.001 TRP A 328 HIS 0.004 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 6266) covalent geometry : angle 0.53071 / 0.27 ( 8501) hydrogen bonds : bond 0.04241 / 2.58 ( 304) hydrogen bonds : angle 3.92118 / 2.76 ( 930) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8776 (ptp-110) cc_final: 0.8516 (mtm110) REVERT: B 104 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7964 (tm-30) REVERT: A 220 MET cc_start: 0.8431 (mmt) cc_final: 0.7503 (mmt) REVERT: A 266 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.6239 (tpp-160) REVERT: A 314 ARG cc_start: 0.7878 (tpp80) cc_final: 0.7256 (mtm-85) REVERT: A 530 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.6841 (mpt) outliers start: 11 outliers final: 6 residues processed: 106 average time/residue: 0.0868 time to fit residues: 11.7497 Evaluate side-chains 105 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 530 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 52 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.066148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.057590 restraints weight = 17983.494| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.62 r_work: 0.2885 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6266 Z= 0.145 Angle : 0.554 7.004 8501 Z= 0.287 Chirality : 0.041 0.138 931 Planarity : 0.004 0.037 1097 Dihedral : 4.451 16.106 915 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.99 % Allowed : 17.00 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: 1.01 (0.31), residues: 763 helix: 1.89 (0.27), residues: 367 sheet: 0.94 (0.51), residues: 108 loop : -1.08 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 71 TYR 0.013 0.002 TYR A 500 PHE 0.013 0.001 PHE B 155 TRP 0.009 0.001 TRP A 328 HIS 0.004 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 6266) covalent geometry : angle 0.55416 / 0.29 ( 8501) hydrogen bonds : bond 0.04607 / 2.80 ( 304) hydrogen bonds : angle 4.00161 / 2.82 ( 930) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8799 (ptp-110) cc_final: 0.8516 (mtm110) REVERT: B 104 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8026 (tm-30) REVERT: A 88 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7523 (tmm) REVERT: A 314 ARG cc_start: 0.8022 (tpp80) cc_final: 0.7405 (mtm-85) outliers start: 13 outliers final: 6 residues processed: 104 average time/residue: 0.1005 time to fit residues: 13.3108 Evaluate side-chains 97 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 511 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 370 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.066307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.057822 restraints weight = 17783.496| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.60 r_work: 0.2894 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6266 Z= 0.141 Angle : 0.559 6.917 8501 Z= 0.288 Chirality : 0.041 0.148 931 Planarity : 0.004 0.035 1097 Dihedral : 4.402 15.985 915 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.30 % Allowed : 17.15 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: 0.94 (0.30), residues: 763 helix: 1.87 (0.27), residues: 366 sheet: 0.79 (0.50), residues: 108 loop : -1.11 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.012 0.002 TYR B 21 PHE 0.012 0.001 PHE B 155 TRP 0.011 0.001 TRP A 328 HIS 0.004 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 6266) covalent geometry : angle 0.55914 / 0.29 ( 8501) hydrogen bonds : bond 0.04411 / 2.69 ( 304) hydrogen bonds : angle 3.93788 / 2.77 ( 930) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8793 (ptp-110) cc_final: 0.8497 (mtm110) REVERT: B 58 ILE cc_start: 0.8169 (mt) cc_final: 0.7929 (pt) REVERT: A 88 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7500 (tmm) REVERT: A 220 MET cc_start: 0.8471 (mmt) cc_final: 0.7711 (mmt) REVERT: A 570 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8984 (mp) outliers start: 15 outliers final: 9 residues processed: 100 average time/residue: 0.0845 time to fit residues: 10.9548 Evaluate side-chains 101 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 570 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 52 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.1980 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.067460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.058990 restraints weight = 17589.710| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.58 r_work: 0.2926 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6266 Z= 0.124 Angle : 0.552 7.053 8501 Z= 0.284 Chirality : 0.041 0.132 931 Planarity : 0.004 0.034 1097 Dihedral : 4.262 15.762 915 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.99 % Allowed : 17.92 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: 1.03 (0.30), residues: 763 helix: 2.00 (0.27), residues: 367 sheet: 0.74 (0.49), residues: 110 loop : -1.13 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 71 TYR 0.010 0.001 TYR A 463 PHE 0.011 0.001 PHE B 155 TRP 0.038 0.002 TRP A 366 HIS 0.003 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 6266) covalent geometry : angle 0.55249 / 0.28 ( 8501) hydrogen bonds : bond 0.03955 / 2.41 ( 304) hydrogen bonds : angle 3.82496 / 2.69 ( 930) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8802 (ptp-110) cc_final: 0.8507 (mtm110) REVERT: B 58 ILE cc_start: 0.8166 (mt) cc_final: 0.7923 (pt) REVERT: A 88 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7418 (tmm) REVERT: A 220 MET cc_start: 0.8460 (mmt) cc_final: 0.7705 (mmt) REVERT: A 432 LYS cc_start: 0.8538 (mtmm) cc_final: 0.8335 (mttp) REVERT: A 570 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8665 (mm) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 0.0843 time to fit residues: 11.5414 Evaluate side-chains 104 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 570 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.065756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.057430 restraints weight = 17648.752| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.56 r_work: 0.2888 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6266 Z= 0.155 Angle : 0.601 7.827 8501 Z= 0.309 Chirality : 0.041 0.133 931 Planarity : 0.004 0.035 1097 Dihedral : 4.411 18.271 915 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.14 % Allowed : 18.38 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: 0.85 (0.30), residues: 763 helix: 1.81 (0.27), residues: 367 sheet: 0.82 (0.50), residues: 107 loop : -1.21 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 71 TYR 0.014 0.002 TYR A 500 PHE 0.013 0.001 PHE B 155 TRP 0.030 0.002 TRP A 366 HIS 0.004 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 6266) covalent geometry : angle 0.60067 / 0.31 ( 8501) hydrogen bonds : bond 0.04680 / 2.85 ( 304) hydrogen bonds : angle 4.06151 / 2.86 ( 930) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.242 Fit side-chains REVERT: B 35 ARG cc_start: 0.8795 (ptp-110) cc_final: 0.8506 (mtm110) REVERT: A 88 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7515 (tmm) REVERT: A 220 MET cc_start: 0.8457 (mmt) cc_final: 0.7682 (mmt) REVERT: A 570 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8643 (mm) outliers start: 14 outliers final: 9 residues processed: 101 average time/residue: 0.0802 time to fit residues: 10.4765 Evaluate side-chains 97 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 570 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 0.0270 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.067253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.058831 restraints weight = 17741.607| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.60 r_work: 0.2923 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6266 Z= 0.132 Angle : 0.597 8.152 8501 Z= 0.306 Chirality : 0.041 0.135 931 Planarity : 0.004 0.034 1097 Dihedral : 4.309 19.157 915 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.68 % Allowed : 19.45 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: 0.98 (0.30), residues: 763 helix: 1.92 (0.27), residues: 367 sheet: 0.83 (0.50), residues: 107 loop : -1.14 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 71 TYR 0.011 0.001 TYR A 463 PHE 0.011 0.001 PHE B 155 TRP 0.034 0.002 TRP A 366 HIS 0.003 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 6266) covalent geometry : angle 0.59657 / 0.31 ( 8501) hydrogen bonds : bond 0.04058 / 2.48 ( 304) hydrogen bonds : angle 3.91382 / 2.75 ( 930) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8787 (ptp-110) cc_final: 0.8507 (mtm110) REVERT: B 58 ILE cc_start: 0.8077 (mt) cc_final: 0.7846 (pt) REVERT: A 88 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7462 (tmm) REVERT: A 220 MET cc_start: 0.8468 (mmt) cc_final: 0.7724 (mmt) REVERT: A 570 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8559 (mm) outliers start: 11 outliers final: 9 residues processed: 95 average time/residue: 0.0799 time to fit residues: 9.8274 Evaluate side-chains 98 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 58 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.066472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.058054 restraints weight = 17660.257| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.58 r_work: 0.2902 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6266 Z= 0.145 Angle : 0.618 8.544 8501 Z= 0.317 Chirality : 0.041 0.134 931 Planarity : 0.004 0.036 1097 Dihedral : 4.337 19.291 915 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.68 % Allowed : 19.75 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: 0.93 (0.30), residues: 763 helix: 1.86 (0.26), residues: 367 sheet: 0.85 (0.50), residues: 105 loop : -1.13 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 71 TYR 0.012 0.002 TYR B 21 PHE 0.012 0.001 PHE B 155 TRP 0.040 0.002 TRP A 366 HIS 0.004 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 6266) covalent geometry : angle 0.61800 / 0.32 ( 8501) hydrogen bonds : bond 0.04428 / 2.69 ( 304) hydrogen bonds : angle 4.00650 / 2.82 ( 930) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8798 (ptp-110) cc_final: 0.8403 (mtm110) REVERT: B 58 ILE cc_start: 0.8118 (mt) cc_final: 0.7879 (pt) REVERT: B 234 MET cc_start: 0.9209 (mmm) cc_final: 0.8982 (mmt) REVERT: A 88 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7501 (tmm) REVERT: A 220 MET cc_start: 0.8435 (mmt) cc_final: 0.7670 (mmt) REVERT: A 570 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8599 (mm) outliers start: 11 outliers final: 9 residues processed: 95 average time/residue: 0.0868 time to fit residues: 10.5658 Evaluate side-chains 99 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 46 optimal weight: 0.0980 chunk 62 optimal weight: 0.6980 chunk 36 optimal weight: 0.0970 chunk 63 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.059513 restraints weight = 17578.582| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.59 r_work: 0.2941 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6266 Z= 0.123 Angle : 0.594 8.237 8501 Z= 0.303 Chirality : 0.041 0.133 931 Planarity : 0.004 0.035 1097 Dihedral : 4.201 19.528 915 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.53 % Allowed : 20.06 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: 1.08 (0.31), residues: 763 helix: 2.00 (0.27), residues: 367 sheet: 0.79 (0.49), residues: 110 loop : -1.05 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 71 TYR 0.021 0.001 TYR B 21 PHE 0.010 0.001 PHE B 155 TRP 0.041 0.002 TRP A 366 HIS 0.003 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 6266) covalent geometry : angle 0.59368 / 0.30 ( 8501) hydrogen bonds : bond 0.03836 / 2.34 ( 304) hydrogen bonds : angle 3.89626 / 2.74 ( 930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1150.86 seconds wall clock time: 20 minutes 25.10 seconds (1225.10 seconds total)