Starting phenix.real_space_refine on Wed Aug 5 02:55:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uuy_64520/08_2026/9uuy_64520.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uuy_64520/08_2026/9uuy_64520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uuy_64520/08_2026/9uuy_64520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uuy_64520/08_2026/9uuy_64520.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uuy_64520/08_2026/9uuy_64520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uuy_64520/08_2026/9uuy_64520.map" } resolution = 3.85 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= 0.000 sd= 0.017 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 54 5.16 5 C 5252 2.51 5 N 1326 2.21 5 O 1410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 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: 8042 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3263 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 2 Chain: "A" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3263 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 2 Chain: "C" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 758 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "D" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 758 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Time building chain proxies: 1.92, per 1000 atoms: 0.24 Number of scatterers: 8042 At special positions: 0 Unit cell: (91.02, 103.32, 107.42, 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 54 16.00 O 1410 8.00 N 1326 7.00 C 5252 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: 0.64 Conformation dependent library (CDL) restraints added in 453.8 milliseconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 2 sheets defined 70.7% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'B' and resid 3 through 23 removed outlier: 4.109A pdb=" N THR B 7 " --> pdb=" O GLY B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 50 Processing helix chain 'B' and resid 56 through 76 Processing helix chain 'B' and resid 82 through 108 Processing helix chain 'B' and resid 114 through 148 removed outlier: 3.781A pdb=" N VAL B 125 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 135 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 181 removed outlier: 3.510A pdb=" N ARG B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 209 removed outlier: 3.554A pdb=" N TRP B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 237 removed outlier: 4.356A pdb=" N SER B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 264 Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 315 through 321 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 450 through 460 Processing helix chain 'A' and resid 4 through 24 removed outlier: 3.713A pdb=" N ALA A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR A 10 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 50 removed outlier: 3.560A pdb=" N GLY A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 47 " --> pdb=" O ILE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 74 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 107 removed outlier: 3.643A pdb=" N LEU A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A 107 " --> pdb=" O PHE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 147 removed outlier: 3.549A pdb=" N THR A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A 141 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 181 Processing helix chain 'A' and resid 183 through 209 removed outlier: 3.587A pdb=" N GLN A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 236 removed outlier: 3.546A pdb=" N VAL A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 263 removed outlier: 3.895A pdb=" N VAL A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 295 through 306 removed outlier: 3.532A pdb=" N GLU A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.999A pdb=" N ALA A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 320 " --> pdb=" O GLY A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.867A pdb=" N VAL A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.882A pdb=" N ALA A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 417 Processing helix chain 'C' and resid 418 through 420 No H-bonds generated for 'chain 'C' and resid 418 through 420' Processing helix chain 'C' and resid 423 through 445 removed outlier: 3.703A pdb=" N HIS C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 462 Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.612A pdb=" N LEU C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 494 removed outlier: 3.534A pdb=" N ASN C 492 " --> pdb=" O ILE C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 504 removed outlier: 3.890A pdb=" N VAL C 499 " --> pdb=" O GLY C 495 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR C 500 " --> pdb=" O GLY C 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 445 removed outlier: 3.872A pdb=" N TRP D 443 " --> pdb=" O TYR D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 462 Processing helix chain 'D' and resid 463 through 473 removed outlier: 3.884A pdb=" N GLY D 467 " --> pdb=" O ILE D 463 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN D 471 " --> pdb=" O GLY D 467 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY D 473 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 504 removed outlier: 3.768A pdb=" N LEU D 481 " --> pdb=" O TRP D 477 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG D 502 " --> pdb=" O THR D 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 339 through 341 removed outlier: 3.822A pdb=" N THR B 384 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 294 removed outlier: 4.206A pdb=" N PHE A 448 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL A 420 " --> pdb=" O HIS A 445 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU A 447 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL A 422 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL A 385 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE A 423 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL A 387 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N SER A 308 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LEU A 386 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE A 310 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE A 388 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 312 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 311 " --> pdb=" O ARG A 341 " (cutoff:3.500A) 547 hydrogen bonds defined for protein. 1623 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: 0.79 Time building geometry restraints manager: 0.85 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: 2530 1.34 - 1.46: 1679 1.46 - 1.58: 3893 1.58 - 1.70: 2 1.70 - 1.81: 102 Bond restraints: 8206 Sorted by residual: bond pdb=" CB PRO A 396 " pdb=" CG PRO A 396 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.33e+00 bond pdb=" N PRO A 396 " pdb=" CA PRO A 396 " ideal model delta sigma weight residual 1.472 1.447 0.025 1.34e-02 5.57e+03 3.35e+00 bond pdb=" CB PRO A 313 " pdb=" CG PRO A 313 " ideal model delta sigma weight residual 1.492 1.580 -0.088 5.00e-02 4.00e+02 3.12e+00 bond pdb=" CG LEU B 359 " pdb=" CD2 LEU B 359 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.89e+00 bond pdb=" CA LEU B 191 " pdb=" C LEU B 191 " ideal model delta sigma weight residual 1.522 1.545 -0.022 1.36e-02 5.41e+03 2.70e+00 ... (remaining 8201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 10931 3.07 - 6.14: 189 6.14 - 9.21: 26 9.21 - 12.28: 3 12.28 - 15.35: 1 Bond angle restraints: 11150 Sorted by residual: angle pdb=" CA PRO A 396 " pdb=" N PRO A 396 " pdb=" CD PRO A 396 " ideal model delta sigma weight residual 112.00 96.65 15.35 1.40e+00 5.10e-01 1.20e+02 angle pdb=" CA PRO A 313 " pdb=" N PRO A 313 " pdb=" CD PRO A 313 " ideal model delta sigma weight residual 112.00 102.31 9.69 1.40e+00 5.10e-01 4.79e+01 angle pdb=" N PRO A 396 " pdb=" CD PRO A 396 " pdb=" CG PRO A 396 " ideal model delta sigma weight residual 103.20 95.62 7.58 1.50e+00 4.44e-01 2.55e+01 angle pdb=" N ALA C 448 " pdb=" CA ALA C 448 " pdb=" C ALA C 448 " ideal model delta sigma weight residual 114.39 107.43 6.96 1.45e+00 4.76e-01 2.30e+01 angle pdb=" N VAL C 419 " pdb=" CA VAL C 419 " pdb=" C VAL C 419 " ideal model delta sigma weight residual 112.83 108.24 4.59 9.90e-01 1.02e+00 2.15e+01 ... (remaining 11145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 4009 17.39 - 34.77: 590 34.77 - 52.16: 168 52.16 - 69.55: 20 69.55 - 86.94: 7 Dihedral angle restraints: 4794 sinusoidal: 1754 harmonic: 3040 Sorted by residual: dihedral pdb=" CA PHE B 342 " pdb=" C PHE B 342 " pdb=" N GLY B 343 " pdb=" CA GLY B 343 " ideal model delta harmonic sigma weight residual -180.00 -147.65 -32.35 0 5.00e+00 4.00e-02 4.19e+01 dihedral pdb=" CA LEU A 370 " pdb=" C LEU A 370 " pdb=" N GLU A 371 " pdb=" CA GLU A 371 " ideal model delta harmonic sigma weight residual -180.00 -156.66 -23.34 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA GLY A 449 " pdb=" C GLY A 449 " pdb=" N ASP A 450 " pdb=" CA ASP A 450 " ideal model delta harmonic sigma weight residual 180.00 -156.93 -23.07 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 4791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 919 0.043 - 0.086: 330 0.086 - 0.129: 84 0.129 - 0.172: 17 0.172 - 0.215: 2 Chirality restraints: 1352 Sorted by residual: chirality pdb=" CG LEU A 61 " pdb=" CB LEU A 61 " pdb=" CD1 LEU A 61 " pdb=" CD2 LEU A 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CG LEU B 359 " pdb=" CB LEU B 359 " pdb=" CD1 LEU B 359 " pdb=" CD2 LEU B 359 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CB VAL B 65 " pdb=" CA VAL B 65 " pdb=" CG1 VAL B 65 " pdb=" CG2 VAL B 65 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.36e-01 ... (remaining 1349 not shown) Planarity restraints: 1382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 395 " -0.110 5.00e-02 4.00e+02 1.55e-01 3.82e+01 pdb=" N PRO A 396 " 0.267 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 312 " -0.104 5.00e-02 4.00e+02 1.50e-01 3.62e+01 pdb=" N PRO A 313 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 342 " -0.025 2.00e-02 2.50e+03 2.36e-02 9.75e+00 pdb=" CG PHE B 342 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE B 342 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 342 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 342 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE B 342 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 342 " -0.004 2.00e-02 2.50e+03 ... (remaining 1379 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 84 2.62 - 3.19: 8070 3.19 - 3.76: 13372 3.76 - 4.33: 17285 4.33 - 4.90: 27730 Nonbonded interactions: 66541 Sorted by model distance: nonbonded pdb=" O ALA A 88 " pdb=" OG SER A 139 " model vdw 2.044 3.040 nonbonded pdb=" O VAL A 101 " pdb=" OG SER A 105 " model vdw 2.122 3.040 nonbonded pdb=" OD1 ASP A 53 " pdb=" N THR A 54 " model vdw 2.137 3.120 nonbonded pdb=" O ALA B 88 " pdb=" OG SER B 139 " model vdw 2.150 3.040 nonbonded pdb=" O ALA A 22 " pdb=" OG SER A 25 " model vdw 2.182 3.040 ... (remaining 66536 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.080 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 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 : 0.005 0.126 8206 Z= 0.220 Angle : 1.030 15.351 11150 Z= 0.614 Chirality : 0.047 0.215 1352 Planarity : 0.009 0.155 1382 Dihedral : 17.620 86.936 2838 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.51 % Favored : 91.02 % Rotamer: Outliers : 0.59 % Allowed : 39.18 % Favored : 60.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.26), residues: 1058 helix: 0.20 (0.20), residues: 691 sheet: -1.66 (1.13), residues: 24 loop : -2.52 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 425 TYR 0.021 0.002 TYR B 324 PHE 0.054 0.002 PHE B 342 TRP 0.031 0.002 TRP A 415 HIS 0.007 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 ( 8206) covalent geometry : angle 1.03010 / 0.61 (11150) hydrogen bonds : bond 0.17287 / 11.72 ( 547) hydrogen bonds : angle 6.79254 / 5.03 ( 1623) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 253 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4821 (ttt) cc_final: 0.4194 (tmm) REVERT: B 423 PHE cc_start: 0.8770 (m-80) cc_final: 0.8530 (m-80) REVERT: B 448 PHE cc_start: 0.7313 (p90) cc_final: 0.7078 (p90) REVERT: A 203 TRP cc_start: 0.5539 (m-10) cc_final: 0.5309 (m100) REVERT: A 328 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8347 (tm-30) REVERT: C 506 MET cc_start: 0.7664 (mmm) cc_final: 0.7195 (mmt) outliers start: 5 outliers final: 5 residues processed: 256 average time/residue: 0.0655 time to fit residues: 24.6551 Evaluate side-chains 236 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 231 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 491 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.0770 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 HIS ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 HIS C 447 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.168092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148561 restraints weight = 13408.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.152638 restraints weight = 6912.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.155329 restraints weight = 4196.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.157113 restraints weight = 2897.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.158259 restraints weight = 2198.439| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8206 Z= 0.170 Angle : 0.766 11.898 11150 Z= 0.386 Chirality : 0.045 0.296 1352 Planarity : 0.006 0.081 1382 Dihedral : 5.845 51.808 1118 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.28 % Favored : 92.34 % Rotamer: Outliers : 5.29 % Allowed : 31.53 % Favored : 63.18 % 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 are not related in a simple way. whole: -0.54 (0.26), residues: 1058 helix: 0.52 (0.19), residues: 718 sheet: -1.86 (1.95), residues: 12 loop : -2.24 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 265 TYR 0.020 0.002 TYR B 324 PHE 0.025 0.002 PHE B 448 TRP 0.014 0.001 TRP A 415 HIS 0.004 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 8206) covalent geometry : angle 0.76554 / 0.39 (11150) hydrogen bonds : bond 0.04518 / 3.09 ( 547) hydrogen bonds : angle 4.88756 / 3.55 ( 1623) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4738 (ttt) cc_final: 0.4052 (tmm) REVERT: B 139 SER cc_start: 0.8911 (t) cc_final: 0.8657 (t) REVERT: B 165 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8404 (mm) REVERT: B 259 MET cc_start: 0.8289 (mmm) cc_final: 0.7894 (mmm) REVERT: B 317 MET cc_start: 0.9150 (mmm) cc_final: 0.8886 (mmm) REVERT: B 371 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6699 (mt-10) REVERT: B 446 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6757 (tmm) REVERT: C 416 MET cc_start: 0.6218 (pmm) cc_final: 0.5956 (pmm) REVERT: C 443 TRP cc_start: 0.6956 (OUTLIER) cc_final: 0.6541 (m100) REVERT: C 477 TRP cc_start: 0.7771 (OUTLIER) cc_final: 0.7135 (t-100) REVERT: D 415 TRP cc_start: 0.8469 (p90) cc_final: 0.8199 (p90) outliers start: 45 outliers final: 22 residues processed: 283 average time/residue: 0.0622 time to fit residues: 26.1653 Evaluate side-chains 261 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain C residue 443 TRP Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 HIS ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.168580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.149038 restraints weight = 13207.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.152968 restraints weight = 6835.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.155678 restraints weight = 4176.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.157313 restraints weight = 2892.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.158607 restraints weight = 2230.078| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8206 Z= 0.159 Angle : 0.729 10.247 11150 Z= 0.369 Chirality : 0.043 0.157 1352 Planarity : 0.006 0.063 1382 Dihedral : 5.600 58.448 1114 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.09 % Favored : 92.63 % Rotamer: Outliers : 6.71 % Allowed : 31.29 % Favored : 62.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.37 (0.26), residues: 1058 helix: 0.64 (0.19), residues: 725 sheet: -1.81 (2.00), residues: 12 loop : -2.20 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 334 TYR 0.022 0.002 TYR B 324 PHE 0.016 0.001 PHE B 19 TRP 0.010 0.001 TRP A 415 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 8206) covalent geometry : angle 0.72864 / 0.37 (11150) hydrogen bonds : bond 0.04213 / 2.86 ( 547) hydrogen bonds : angle 4.64587 / 3.37 ( 1623) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 252 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4449 (ttt) cc_final: 0.4153 (tmm) REVERT: B 139 SER cc_start: 0.8746 (t) cc_final: 0.8493 (t) REVERT: B 165 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8197 (mm) REVERT: A 45 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7206 (mp) REVERT: A 100 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7722 (mm) REVERT: A 201 PHE cc_start: 0.8286 (t80) cc_final: 0.7996 (t80) REVERT: A 220 MET cc_start: 0.7751 (tmm) cc_final: 0.7210 (tmm) REVERT: A 443 ASN cc_start: 0.7912 (t0) cc_final: 0.7708 (t0) REVERT: C 443 TRP cc_start: 0.7056 (OUTLIER) cc_final: 0.6463 (m100) REVERT: D 415 TRP cc_start: 0.8447 (p90) cc_final: 0.8233 (p90) REVERT: D 503 MET cc_start: 0.8172 (tmm) cc_final: 0.7967 (tmm) outliers start: 57 outliers final: 35 residues processed: 280 average time/residue: 0.0564 time to fit residues: 23.8143 Evaluate side-chains 278 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 443 TRP Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 443 TRP Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 80 optimal weight: 0.3980 chunk 2 optimal weight: 0.0270 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** B 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.167034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148989 restraints weight = 13360.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.152438 restraints weight = 7404.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.154876 restraints weight = 4753.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.156555 restraints weight = 3367.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.157526 restraints weight = 2597.782| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8206 Z= 0.150 Angle : 0.718 12.578 11150 Z= 0.362 Chirality : 0.043 0.178 1352 Planarity : 0.005 0.057 1382 Dihedral : 5.520 59.555 1114 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.18 % Favored : 92.53 % Rotamer: Outliers : 7.65 % Allowed : 30.71 % Favored : 61.65 % 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 are not related in a simple way. whole: -0.20 (0.26), residues: 1058 helix: 0.75 (0.19), residues: 726 sheet: -1.64 (2.04), residues: 12 loop : -2.11 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 334 TYR 0.018 0.002 TYR B 324 PHE 0.025 0.001 PHE A 126 TRP 0.007 0.001 TRP C 477 HIS 0.006 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 8206) covalent geometry : angle 0.71832 / 0.36 (11150) hydrogen bonds : bond 0.04088 / 2.77 ( 547) hydrogen bonds : angle 4.51969 / 3.30 ( 1623) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 245 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8263 (t) REVERT: B 259 MET cc_start: 0.7994 (mmm) cc_final: 0.7776 (mmm) REVERT: A 83 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7884 (tpp) REVERT: A 100 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7703 (mm) REVERT: A 127 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8308 (tt) REVERT: A 161 HIS cc_start: 0.6254 (OUTLIER) cc_final: 0.5833 (m-70) REVERT: A 220 MET cc_start: 0.7857 (tmm) cc_final: 0.7292 (tmm) REVERT: A 317 MET cc_start: 0.8313 (mtp) cc_final: 0.8062 (ttm) REVERT: C 416 MET cc_start: 0.5915 (pmm) cc_final: 0.5681 (pmm) REVERT: C 443 TRP cc_start: 0.7037 (OUTLIER) cc_final: 0.6530 (m100) outliers start: 65 outliers final: 36 residues processed: 280 average time/residue: 0.0693 time to fit residues: 29.2160 Evaluate side-chains 269 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 443 TRP Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 443 TRP Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 15 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 17 optimal weight: 0.0040 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 ASN ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.166852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148600 restraints weight = 13328.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.152147 restraints weight = 7332.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.154546 restraints weight = 4677.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.156149 restraints weight = 3324.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.157186 restraints weight = 2581.388| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8206 Z= 0.152 Angle : 0.714 11.542 11150 Z= 0.360 Chirality : 0.042 0.191 1352 Planarity : 0.005 0.057 1382 Dihedral : 5.460 59.508 1114 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.56 % Favored : 92.16 % Rotamer: Outliers : 6.94 % Allowed : 30.47 % Favored : 62.59 % 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 are not related in a simple way. whole: -0.04 (0.26), residues: 1058 helix: 0.86 (0.19), residues: 728 sheet: -1.24 (2.00), residues: 12 loop : -2.04 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 350 TYR 0.016 0.002 TYR A 10 PHE 0.022 0.001 PHE B 36 TRP 0.007 0.001 TRP A 203 HIS 0.005 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 8206) covalent geometry : angle 0.71406 / 0.36 (11150) hydrogen bonds : bond 0.04046 / 2.77 ( 547) hydrogen bonds : angle 4.46718 / 3.26 ( 1623) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 246 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: B 139 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8177 (t) REVERT: B 382 THR cc_start: 0.7922 (m) cc_final: 0.7693 (m) REVERT: A 18 ILE cc_start: 0.8833 (tt) cc_final: 0.8544 (tp) REVERT: A 45 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6907 (mp) REVERT: A 100 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7733 (mm) REVERT: A 103 PHE cc_start: 0.8036 (t80) cc_final: 0.7753 (t80) REVERT: A 127 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8328 (tt) REVERT: A 161 HIS cc_start: 0.6210 (OUTLIER) cc_final: 0.5779 (m-70) REVERT: A 220 MET cc_start: 0.7890 (tmm) cc_final: 0.7293 (tmm) REVERT: A 301 GLU cc_start: 0.8091 (tp30) cc_final: 0.7674 (tp30) REVERT: A 317 MET cc_start: 0.8243 (mtp) cc_final: 0.7791 (ttm) REVERT: A 443 ASN cc_start: 0.7877 (t0) cc_final: 0.7659 (t0) REVERT: A 450 ASP cc_start: 0.6550 (OUTLIER) cc_final: 0.6009 (m-30) REVERT: C 443 TRP cc_start: 0.7058 (OUTLIER) cc_final: 0.6477 (m100) outliers start: 59 outliers final: 37 residues processed: 275 average time/residue: 0.0703 time to fit residues: 28.3493 Evaluate side-chains 269 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 415 TRP Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 443 TRP Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 443 TRP Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 HIS ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN A 376 ASN ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.159421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140235 restraints weight = 13285.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143727 restraints weight = 7345.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.146089 restraints weight = 4719.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147682 restraints weight = 3401.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.148781 restraints weight = 2673.906| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8206 Z= 0.176 Angle : 0.750 14.725 11150 Z= 0.376 Chirality : 0.044 0.227 1352 Planarity : 0.005 0.059 1382 Dihedral : 5.474 59.694 1114 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.56 % Favored : 92.25 % Rotamer: Outliers : 7.18 % Allowed : 30.12 % Favored : 62.71 % 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 are not related in a simple way. whole: -0.04 (0.26), residues: 1058 helix: 0.92 (0.19), residues: 721 sheet: -2.21 (0.74), residues: 48 loop : -2.01 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 350 TYR 0.019 0.002 TYR B 106 PHE 0.018 0.001 PHE B 36 TRP 0.007 0.001 TRP A 415 HIS 0.005 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 8206) covalent geometry : angle 0.75016 / 0.38 (11150) hydrogen bonds : bond 0.04150 / 2.82 ( 547) hydrogen bonds : angle 4.59267 / 3.36 ( 1623) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 239 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: B 139 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8400 (t) REVERT: B 259 MET cc_start: 0.8052 (mmm) cc_final: 0.7814 (mmm) REVERT: B 372 MET cc_start: 0.7841 (mmm) cc_final: 0.7400 (mmm) REVERT: B 382 THR cc_start: 0.8067 (m) cc_final: 0.7860 (m) REVERT: A 45 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7193 (mp) REVERT: A 100 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7755 (mm) REVERT: A 127 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8207 (tt) REVERT: A 161 HIS cc_start: 0.6192 (OUTLIER) cc_final: 0.5829 (m-70) REVERT: A 220 MET cc_start: 0.7835 (tmm) cc_final: 0.7234 (tmm) REVERT: A 301 GLU cc_start: 0.8241 (tp30) cc_final: 0.7748 (tp30) REVERT: A 317 MET cc_start: 0.8361 (mtp) cc_final: 0.7905 (ttm) REVERT: A 331 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8386 (tp30) REVERT: A 443 ASN cc_start: 0.8015 (t0) cc_final: 0.7770 (t0) REVERT: A 448 PHE cc_start: 0.6691 (m-10) cc_final: 0.6420 (m-10) REVERT: C 443 TRP cc_start: 0.7112 (OUTLIER) cc_final: 0.6485 (m100) outliers start: 61 outliers final: 41 residues processed: 271 average time/residue: 0.0688 time to fit residues: 27.5847 Evaluate side-chains 265 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 218 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 415 TRP Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 443 TRP Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 443 TRP Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 506 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 89 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** B 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.165888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147416 restraints weight = 13166.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.151045 restraints weight = 7163.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.153472 restraints weight = 4503.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.155142 restraints weight = 3185.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.156135 restraints weight = 2460.948| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8206 Z= 0.162 Angle : 0.753 14.159 11150 Z= 0.374 Chirality : 0.044 0.203 1352 Planarity : 0.005 0.059 1382 Dihedral : 5.462 58.836 1114 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.66 % Favored : 92.06 % Rotamer: Outliers : 6.59 % Allowed : 31.18 % Favored : 62.24 % 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 are not related in a simple way. whole: -0.03 (0.26), residues: 1058 helix: 0.91 (0.19), residues: 720 sheet: -2.07 (0.75), residues: 48 loop : -1.98 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 350 TYR 0.011 0.002 TYR A 10 PHE 0.025 0.001 PHE B 19 TRP 0.010 0.001 TRP B 415 HIS 0.005 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 8206) covalent geometry : angle 0.75257 / 0.37 (11150) hydrogen bonds : bond 0.04137 / 2.83 ( 547) hydrogen bonds : angle 4.56373 / 3.34 ( 1623) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: B 139 SER cc_start: 0.8615 (OUTLIER) cc_final: 0.8328 (t) REVERT: B 382 THR cc_start: 0.7970 (m) cc_final: 0.7764 (m) REVERT: B 395 ASN cc_start: 0.8356 (t0) cc_final: 0.7961 (m-40) REVERT: A 45 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7159 (mp) REVERT: A 103 PHE cc_start: 0.8026 (t80) cc_final: 0.7717 (t80) REVERT: A 127 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8232 (tt) REVERT: A 161 HIS cc_start: 0.6164 (OUTLIER) cc_final: 0.5809 (m-70) REVERT: A 220 MET cc_start: 0.7881 (tmm) cc_final: 0.7243 (tmm) REVERT: A 301 GLU cc_start: 0.8153 (tp30) cc_final: 0.7692 (tp30) REVERT: A 317 MET cc_start: 0.8236 (mtp) cc_final: 0.7873 (ttm) REVERT: C 443 TRP cc_start: 0.7068 (OUTLIER) cc_final: 0.6456 (m100) outliers start: 56 outliers final: 42 residues processed: 258 average time/residue: 0.0669 time to fit residues: 25.7723 Evaluate side-chains 275 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 415 TRP Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 443 TRP Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 443 TRP Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 506 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.165148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146586 restraints weight = 13278.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.150134 restraints weight = 7265.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152567 restraints weight = 4615.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.154244 restraints weight = 3282.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.155337 restraints weight = 2543.765| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8206 Z= 0.169 Angle : 0.776 14.238 11150 Z= 0.385 Chirality : 0.044 0.211 1352 Planarity : 0.005 0.059 1382 Dihedral : 5.447 58.789 1114 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.37 % Favored : 92.44 % Rotamer: Outliers : 6.12 % Allowed : 31.76 % Favored : 62.12 % 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 are not related in a simple way. whole: -0.04 (0.26), residues: 1058 helix: 0.90 (0.19), residues: 720 sheet: -2.06 (0.75), residues: 48 loop : -1.96 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 425 TYR 0.020 0.002 TYR A 10 PHE 0.019 0.001 PHE A 126 TRP 0.009 0.001 TRP C 477 HIS 0.006 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 8206) covalent geometry : angle 0.77569 / 0.39 (11150) hydrogen bonds : bond 0.04149 / 2.85 ( 547) hydrogen bonds : angle 4.61247 / 3.38 ( 1623) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 238 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: B 139 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8346 (t) REVERT: B 395 ASN cc_start: 0.8393 (t0) cc_final: 0.8165 (m-40) REVERT: A 45 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7226 (mp) REVERT: A 85 GLU cc_start: 0.8259 (mp0) cc_final: 0.8046 (mm-30) REVERT: A 100 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7637 (mm) REVERT: A 103 PHE cc_start: 0.8073 (t80) cc_final: 0.7708 (t80) REVERT: A 127 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8104 (tt) REVERT: A 161 HIS cc_start: 0.6089 (OUTLIER) cc_final: 0.5802 (m170) REVERT: A 220 MET cc_start: 0.7902 (tmm) cc_final: 0.7371 (tmm) REVERT: A 328 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7992 (tm-30) REVERT: C 443 TRP cc_start: 0.7083 (OUTLIER) cc_final: 0.6462 (m100) REVERT: C 503 MET cc_start: 0.7545 (tpp) cc_final: 0.7233 (tpp) REVERT: D 503 MET cc_start: 0.8041 (tmm) cc_final: 0.7608 (tmm) outliers start: 52 outliers final: 42 residues processed: 261 average time/residue: 0.0625 time to fit residues: 24.9563 Evaluate side-chains 279 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 231 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 415 TRP Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 443 TRP Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 506 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 ASN ** 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 = 0.3894 r_free = 0.3894 target = 0.162594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.144225 restraints weight = 13259.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.147755 restraints weight = 7177.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.150193 restraints weight = 4515.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.151901 restraints weight = 3178.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.153062 restraints weight = 2436.306| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8206 Z= 0.193 Angle : 0.789 14.071 11150 Z= 0.392 Chirality : 0.044 0.224 1352 Planarity : 0.005 0.060 1382 Dihedral : 5.450 58.134 1114 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.75 % Favored : 92.06 % Rotamer: Outliers : 6.59 % Allowed : 31.88 % Favored : 61.53 % 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 are not related in a simple way. whole: -0.03 (0.26), residues: 1058 helix: 0.91 (0.19), residues: 720 sheet: -2.05 (0.74), residues: 48 loop : -1.97 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 350 TYR 0.016 0.002 TYR A 10 PHE 0.018 0.002 PHE B 19 TRP 0.007 0.001 TRP A 415 HIS 0.006 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 ( 8206) covalent geometry : angle 0.78877 / 0.39 (11150) hydrogen bonds : bond 0.04213 / 2.87 ( 547) hydrogen bonds : angle 4.68859 / 3.44 ( 1623) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 232 time to evaluate : 0.354 Fit side-chains REVERT: B 139 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8480 (t) REVERT: B 395 ASN cc_start: 0.8421 (t0) cc_final: 0.8215 (m-40) REVERT: A 45 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7321 (mp) REVERT: A 85 GLU cc_start: 0.8369 (mp0) cc_final: 0.8126 (mm-30) REVERT: A 100 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7617 (mm) REVERT: A 106 TYR cc_start: 0.8508 (t80) cc_final: 0.8115 (t80) REVERT: A 127 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8244 (tt) REVERT: A 161 HIS cc_start: 0.6048 (OUTLIER) cc_final: 0.5818 (m170) REVERT: A 194 MET cc_start: 0.8312 (tmm) cc_final: 0.8060 (tmm) REVERT: A 220 MET cc_start: 0.7960 (tmm) cc_final: 0.7403 (tmm) REVERT: A 328 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8063 (tm-30) REVERT: A 448 PHE cc_start: 0.6852 (m-10) cc_final: 0.6426 (m-10) REVERT: C 443 TRP cc_start: 0.7084 (OUTLIER) cc_final: 0.6452 (m100) outliers start: 56 outliers final: 46 residues processed: 257 average time/residue: 0.0640 time to fit residues: 25.0960 Evaluate side-chains 273 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 221 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 415 TRP Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 443 TRP Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 443 TRP Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 506 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 101 optimal weight: 0.2980 chunk 100 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 ASN ** 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 = 0.3942 r_free = 0.3942 target = 0.167084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148861 restraints weight = 13147.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.152543 restraints weight = 7090.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.154980 restraints weight = 4404.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.156598 restraints weight = 3086.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.157802 restraints weight = 2367.747| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8206 Z= 0.159 Angle : 0.775 15.868 11150 Z= 0.384 Chirality : 0.044 0.172 1352 Planarity : 0.005 0.060 1382 Dihedral : 5.440 56.642 1114 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.18 % Favored : 92.63 % Rotamer: Outliers : 6.12 % Allowed : 32.35 % Favored : 61.53 % 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 are not related in a simple way. whole: -0.04 (0.26), residues: 1058 helix: 0.89 (0.19), residues: 717 sheet: -2.02 (0.74), residues: 48 loop : -1.92 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 350 TYR 0.018 0.002 TYR B 324 PHE 0.013 0.001 PHE B 342 TRP 0.007 0.001 TRP C 477 HIS 0.005 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 8206) covalent geometry : angle 0.77475 / 0.38 (11150) hydrogen bonds : bond 0.04115 / 2.82 ( 547) hydrogen bonds : angle 4.63748 / 3.41 ( 1623) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 242 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: B 139 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8350 (t) REVERT: A 45 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7275 (mp) REVERT: A 106 TYR cc_start: 0.8522 (t80) cc_final: 0.8182 (t80) REVERT: A 127 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8334 (tt) REVERT: A 161 HIS cc_start: 0.6003 (OUTLIER) cc_final: 0.5753 (m170) REVERT: A 201 PHE cc_start: 0.8300 (t80) cc_final: 0.8093 (t80) REVERT: A 220 MET cc_start: 0.7905 (tmm) cc_final: 0.7298 (tmm) REVERT: A 301 GLU cc_start: 0.8092 (tp30) cc_final: 0.7660 (tp30) REVERT: A 328 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8107 (tm-30) REVERT: A 448 PHE cc_start: 0.6601 (m-10) cc_final: 0.6225 (m-10) REVERT: C 443 TRP cc_start: 0.7052 (OUTLIER) cc_final: 0.6440 (m100) outliers start: 52 outliers final: 44 residues processed: 264 average time/residue: 0.0587 time to fit residues: 24.1240 Evaluate side-chains 280 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 415 TRP Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 443 TRP Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 443 TRP Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 506 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.0770 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 15 optimal weight: 0.0000 chunk 83 optimal weight: 0.9990 overall best weight: 0.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.163359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144799 restraints weight = 13266.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148223 restraints weight = 7426.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150429 restraints weight = 4785.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.152173 restraints weight = 3479.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.153174 restraints weight = 2710.769| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8206 Z= 0.159 Angle : 0.798 15.567 11150 Z= 0.394 Chirality : 0.045 0.189 1352 Planarity : 0.005 0.059 1382 Dihedral : 5.424 57.807 1114 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.47 % Favored : 92.34 % Rotamer: Outliers : 5.41 % Allowed : 32.47 % Favored : 62.12 % 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 are not related in a simple way. whole: -0.05 (0.26), residues: 1058 helix: 0.88 (0.19), residues: 717 sheet: -1.82 (0.75), residues: 48 loop : -1.95 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 350 TYR 0.020 0.002 TYR A 10 PHE 0.035 0.001 PHE B 36 TRP 0.007 0.001 TRP C 477 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 8206) covalent geometry : angle 0.79754 / 0.39 (11150) hydrogen bonds : bond 0.04152 / 2.86 ( 547) hydrogen bonds : angle 4.64768 / 3.43 ( 1623) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1446.38 seconds wall clock time: 25 minutes 47.41 seconds (1547.41 seconds total)