Starting phenix.real_space_refine on Fri Jan 17 01:02:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xek_38292/01_2025/8xek_38292_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xek_38292/01_2025/8xek_38292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xek_38292/01_2025/8xek_38292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xek_38292/01_2025/8xek_38292.map" model { file = "/net/cci-nas-00/data/ceres_data/8xek_38292/01_2025/8xek_38292_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xek_38292/01_2025/8xek_38292_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.007 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: 5 Type Number sf(0) Gaussians S 56 5.16 5 C 5207 2.51 5 N 1411 2.21 5 O 1616 1.98 5 H 1840 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10130 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 5600 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 28, 'TRANS': 563} Chain: "B" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 4530 Classifications: {'peptide': 481} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 25, 'TRANS': 452} Time building chain proxies: 7.68, per 1000 atoms: 0.76 Number of scatterers: 10130 At special positions: 0 Unit cell: (66, 102.3, 132.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 O 1616 8.00 N 1411 7.00 C 5207 6.00 H 1840 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS A 508 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 39 " - pdb=" SG CYS B 461 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 64 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 210 " distance=2.03 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 459 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 497 " distance=2.03 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: 2.47 Conformation dependent library (CDL) restraints added in 1.0 seconds 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 19 sheets defined 17.1% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.684A pdb=" N LYS A 400 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 534 Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.070A pdb=" N ARG B 34 " --> pdb=" O CYS B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 46 removed outlier: 4.323A pdb=" N ALA B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER B 46 " --> pdb=" O CYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 73 removed outlier: 3.748A pdb=" N LEU B 71 " --> pdb=" O LYS B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.829A pdb=" N LYS B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 225 through 234 removed outlier: 3.855A pdb=" N PHE B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 258 removed outlier: 3.802A pdb=" N ALA B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 307 through 312 removed outlier: 4.265A pdb=" N THR B 311 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 329 Processing helix chain 'B' and resid 340 through 350 removed outlier: 3.857A pdb=" N LEU B 350 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 378 Processing helix chain 'B' and resid 461 through 467 Processing helix chain 'B' and resid 474 through 477 removed outlier: 3.631A pdb=" N GLY B 477 " --> pdb=" O CYS B 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 474 through 477' Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42 removed outlier: 4.420A pdb=" N THR A 442 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE A 453 " --> pdb=" O GLY A 440 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLY A 440 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLY A 455 " --> pdb=" O MET A 438 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N MET A 438 " --> pdb=" O GLY A 455 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 111 removed outlier: 7.192A pdb=" N ASP A 114 " --> pdb=" O TYR A 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.683A pdb=" N HIS A 143 " --> pdb=" O PHE A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA6, first strand: chain 'A' and resid 190 through 193 removed outlier: 3.663A pdb=" N SER A 190 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 256 through 259 removed outlier: 6.402A pdb=" N VAL A 283 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN A 296 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 285 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 313 Processing sheet with id=AA9, first strand: chain 'A' and resid 331 through 333 Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378 removed outlier: 6.579A pdb=" N ILE A 374 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA A 391 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA A 389 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 378 " --> pdb=" O ASP A 387 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 374 through 378 removed outlier: 6.579A pdb=" N ILE A 374 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA A 391 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA A 389 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 378 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A 419 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 541 through 543 removed outlier: 3.508A pdb=" N GLN A 564 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 483 through 485 Processing sheet with id=AB5, first strand: chain 'A' and resid 491 through 492 removed outlier: 3.651A pdb=" N CYS A 491 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AB7, first strand: chain 'B' and resid 86 through 91 removed outlier: 6.395A pdb=" N ARG B 113 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE B 114 " --> pdb=" O GLN B 454 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N THR B 456 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU B 116 " --> pdb=" O THR B 456 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 109 through 110 removed outlier: 4.207A pdb=" N SER B 422 " --> pdb=" O THR B 399 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 216 through 223 removed outlier: 7.049A pdb=" N VAL B 219 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N ALA B 181 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N THR B 221 " --> pdb=" O PHE B 179 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N PHE B 179 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N THR B 355 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 332 " --> pdb=" O THR B 355 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N GLY B 357 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE B 334 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 468 through 471 removed outlier: 3.638A pdb=" N GLU B 468 " --> pdb=" O PHE B 481 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN B 470 " --> pdb=" O GLY B 479 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLY B 479 " --> pdb=" O ASN B 470 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 711 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: 3.55 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 1840 1.03 - 1.23: 19 1.23 - 1.42: 3547 1.42 - 1.62: 4817 1.62 - 1.81: 79 Bond restraints: 10302 Sorted by residual: bond pdb=" N GLY B 27 " pdb=" CA GLY B 27 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.28e+00 bond pdb=" N ASN A 32 " pdb=" CA ASN A 32 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.52e+00 bond pdb=" N GLY B 27 " pdb=" H GLY B 27 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" N ASN A 32 " pdb=" H ASN A 32 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C ALA A 375 " pdb=" O ALA A 375 " ideal model delta sigma weight residual 1.249 1.236 0.013 8.50e-03 1.38e+04 2.22e+00 ... (remaining 10297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 14602 1.95 - 3.89: 135 3.89 - 5.84: 16 5.84 - 7.78: 1 7.78 - 9.73: 2 Bond angle restraints: 14756 Sorted by residual: angle pdb=" C GLU B 502 " pdb=" N ASP B 503 " pdb=" CA ASP B 503 " ideal model delta sigma weight residual 121.70 131.43 -9.73 1.80e+00 3.09e-01 2.92e+01 angle pdb=" CG ARG B 473 " pdb=" CD ARG B 473 " pdb=" NE ARG B 473 " ideal model delta sigma weight residual 112.00 119.79 -7.79 2.20e+00 2.07e-01 1.25e+01 angle pdb=" CA ARG B 473 " pdb=" CB ARG B 473 " pdb=" CG ARG B 473 " ideal model delta sigma weight residual 114.10 119.91 -5.81 2.00e+00 2.50e-01 8.44e+00 angle pdb=" CA GLN B 464 " pdb=" CB GLN B 464 " pdb=" CG GLN B 464 " ideal model delta sigma weight residual 114.10 119.43 -5.33 2.00e+00 2.50e-01 7.10e+00 angle pdb=" C ASN A 485 " pdb=" CA ASN A 485 " pdb=" CB ASN A 485 " ideal model delta sigma weight residual 109.53 113.90 -4.37 1.65e+00 3.67e-01 7.00e+00 ... (remaining 14751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 5998 16.73 - 33.45: 409 33.45 - 50.18: 112 50.18 - 66.90: 42 66.90 - 83.63: 15 Dihedral angle restraints: 6576 sinusoidal: 3473 harmonic: 3103 Sorted by residual: dihedral pdb=" CB CYS B 488 " pdb=" SG CYS B 488 " pdb=" SG CYS B 497 " pdb=" CB CYS B 497 " ideal model delta sinusoidal sigma weight residual 93.00 154.31 -61.31 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CB CYS A 172 " pdb=" SG CYS A 172 " pdb=" SG CYS A 185 " pdb=" CB CYS A 185 " ideal model delta sinusoidal sigma weight residual 93.00 52.13 40.87 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CB CYS B 474 " pdb=" SG CYS B 474 " pdb=" SG CYS B 486 " pdb=" CB CYS B 486 " ideal model delta sinusoidal sigma weight residual -86.00 -120.47 34.47 1 1.00e+01 1.00e-02 1.69e+01 ... (remaining 6573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 879 0.038 - 0.075: 253 0.075 - 0.113: 91 0.113 - 0.150: 28 0.150 - 0.188: 1 Chirality restraints: 1252 Sorted by residual: chirality pdb=" CA SER B 194 " pdb=" N SER B 194 " pdb=" C SER B 194 " pdb=" CB SER B 194 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA PRO B 47 " pdb=" N PRO B 47 " pdb=" C PRO B 47 " pdb=" CB PRO B 47 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE B 406 " pdb=" N ILE B 406 " pdb=" C ILE B 406 " pdb=" CB ILE B 406 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1249 not shown) Planarity restraints: 2535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 592 " 0.189 9.50e-02 1.11e+02 6.34e-02 4.99e+00 pdb=" NE ARG A 592 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 592 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 592 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 592 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 592 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 592 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 592 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 592 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 194 " 0.028 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO B 195 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 195 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 195 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 46 " -0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 47 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 47 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 47 " -0.021 5.00e-02 4.00e+02 ... (remaining 2532 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 199 2.06 - 2.70: 4913 2.70 - 3.33: 17186 3.33 - 3.97: 23920 3.97 - 4.60: 35184 Nonbonded interactions: 81402 Sorted by model distance: nonbonded pdb=" OE1 GLU B 390 " pdb=" H GLU B 390 " model vdw 1.427 2.450 nonbonded pdb=" OE1 GLU B 260 " pdb=" H GLU B 260 " model vdw 1.499 2.450 nonbonded pdb=" OD1 ASP A 383 " pdb=" H PHE A 385 " model vdw 1.530 2.450 nonbonded pdb=" OE1 GLN B 434 " pdb=" H GLN B 434 " model vdw 1.545 2.450 nonbonded pdb=" OD2 ASP B 205 " pdb="HH12 ARG B 240 " model vdw 1.597 2.450 ... (remaining 81397 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 26.770 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:13.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 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 : 0.004 0.055 8462 Z= 0.233 Angle : 0.578 9.729 11463 Z= 0.325 Chirality : 0.043 0.188 1252 Planarity : 0.004 0.084 1519 Dihedral : 14.007 83.625 3132 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.22 % Allowed : 11.42 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 1069 helix: 0.08 (0.54), residues: 102 sheet: 1.07 (0.29), residues: 338 loop : -0.13 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 264 HIS 0.005 0.001 HIS B 472 PHE 0.008 0.001 PHE A 193 TYR 0.012 0.001 TYR B 204 ARG 0.016 0.001 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 TRP cc_start: 0.7818 (t-100) cc_final: 0.7074 (t-100) outliers start: 2 outliers final: 2 residues processed: 54 average time/residue: 1.6182 time to fit residues: 93.5697 Evaluate side-chains 51 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 529 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN A 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.092886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.059985 restraints weight = 23522.154| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.65 r_work: 0.2650 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 8462 Z= 0.481 Angle : 0.580 5.047 11463 Z= 0.308 Chirality : 0.047 0.176 1252 Planarity : 0.004 0.038 1519 Dihedral : 5.211 52.785 1167 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.65 % Allowed : 10.54 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1069 helix: -0.39 (0.50), residues: 110 sheet: 0.83 (0.28), residues: 327 loop : -0.18 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 91 HIS 0.005 0.001 HIS B 281 PHE 0.015 0.002 PHE A 306 TYR 0.014 0.002 TYR A 394 ARG 0.004 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ASP cc_start: 0.7510 (t0) cc_final: 0.7300 (t0) outliers start: 15 outliers final: 5 residues processed: 57 average time/residue: 1.6317 time to fit residues: 99.5511 Evaluate side-chains 55 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 432 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.094651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.061728 restraints weight = 23768.149| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.67 r_work: 0.2691 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8462 Z= 0.217 Angle : 0.475 8.334 11463 Z= 0.253 Chirality : 0.043 0.192 1252 Planarity : 0.003 0.033 1519 Dihedral : 4.759 52.132 1167 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.87 % Allowed : 11.20 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1069 helix: -0.06 (0.50), residues: 109 sheet: 0.92 (0.28), residues: 332 loop : -0.22 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 91 HIS 0.002 0.001 HIS B 281 PHE 0.009 0.001 PHE B 274 TYR 0.010 0.001 TYR A 545 ARG 0.002 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8470 (pptt) REVERT: A 528 LEU cc_start: 0.8636 (pt) cc_final: 0.8331 (mt) REVERT: A 563 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8557 (tpt) REVERT: B 51 TRP cc_start: 0.7588 (t-100) cc_final: 0.7221 (t-100) outliers start: 17 outliers final: 4 residues processed: 64 average time/residue: 1.4949 time to fit residues: 102.9694 Evaluate side-chains 53 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 401 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 0.0370 chunk 75 optimal weight: 0.0470 chunk 11 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.094969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.062246 restraints weight = 23498.421| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.65 r_work: 0.2691 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8462 Z= 0.208 Angle : 0.465 7.057 11463 Z= 0.246 Chirality : 0.042 0.141 1252 Planarity : 0.003 0.031 1519 Dihedral : 4.632 51.292 1167 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.87 % Allowed : 12.29 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1069 helix: 0.14 (0.50), residues: 111 sheet: 0.86 (0.28), residues: 332 loop : -0.18 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 209 HIS 0.002 0.000 HIS B 281 PHE 0.008 0.001 PHE B 274 TYR 0.010 0.001 TYR B 344 ARG 0.002 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 480 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.7329 (m-10) REVERT: A 520 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8472 (pptt) outliers start: 17 outliers final: 8 residues processed: 61 average time/residue: 1.4332 time to fit residues: 94.5083 Evaluate side-chains 60 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 480 TYR Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 432 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 51 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.092798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.059980 restraints weight = 23827.743| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.65 r_work: 0.2670 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 8462 Z= 0.395 Angle : 0.530 7.475 11463 Z= 0.279 Chirality : 0.045 0.176 1252 Planarity : 0.003 0.030 1519 Dihedral : 4.998 53.540 1167 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.76 % Allowed : 13.06 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1069 helix: -0.06 (0.50), residues: 110 sheet: 0.72 (0.28), residues: 334 loop : -0.27 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 264 HIS 0.004 0.001 HIS B 281 PHE 0.014 0.001 PHE A 306 TYR 0.012 0.001 TYR A 394 ARG 0.004 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8655 (ptpp) outliers start: 16 outliers final: 9 residues processed: 61 average time/residue: 1.4943 time to fit residues: 97.9130 Evaluate side-chains 56 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 432 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 77 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 96 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN A 212 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.093169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.060333 restraints weight = 23911.670| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.67 r_work: 0.2666 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8462 Z= 0.299 Angle : 0.512 11.678 11463 Z= 0.268 Chirality : 0.044 0.239 1252 Planarity : 0.003 0.028 1519 Dihedral : 4.854 53.298 1167 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.98 % Allowed : 13.50 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1069 helix: 0.06 (0.50), residues: 111 sheet: 0.70 (0.28), residues: 336 loop : -0.24 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 264 HIS 0.003 0.001 HIS B 281 PHE 0.010 0.001 PHE A 306 TYR 0.013 0.001 TYR B 204 ARG 0.003 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8651 (ptpp) outliers start: 18 outliers final: 12 residues processed: 64 average time/residue: 1.5115 time to fit residues: 103.7669 Evaluate side-chains 60 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 432 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 45 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.093439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.060640 restraints weight = 23937.572| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.67 r_work: 0.2669 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8462 Z= 0.264 Angle : 0.501 11.203 11463 Z= 0.262 Chirality : 0.044 0.231 1252 Planarity : 0.003 0.028 1519 Dihedral : 4.751 52.848 1167 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.41 % Allowed : 13.17 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1069 helix: 0.17 (0.50), residues: 111 sheet: 0.69 (0.28), residues: 335 loop : -0.24 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 264 HIS 0.003 0.001 HIS B 281 PHE 0.010 0.001 PHE B 274 TYR 0.013 0.001 TYR B 204 ARG 0.002 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8031 (tmt90) REVERT: A 563 MET cc_start: 0.8758 (tpp) cc_final: 0.8541 (ttt) REVERT: B 51 TRP cc_start: 0.7439 (t-100) cc_final: 0.7233 (t-100) outliers start: 22 outliers final: 14 residues processed: 69 average time/residue: 1.4739 time to fit residues: 109.2300 Evaluate side-chains 64 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 508 CYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 432 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 69 optimal weight: 0.3980 chunk 105 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.094259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.061523 restraints weight = 23783.302| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.67 r_work: 0.2682 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8462 Z= 0.202 Angle : 0.484 10.393 11463 Z= 0.252 Chirality : 0.043 0.203 1252 Planarity : 0.003 0.026 1519 Dihedral : 4.586 51.864 1167 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.65 % Allowed : 14.05 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1069 helix: 0.44 (0.51), residues: 111 sheet: 0.71 (0.28), residues: 337 loop : -0.15 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 209 HIS 0.002 0.000 HIS B 281 PHE 0.009 0.001 PHE B 274 TYR 0.015 0.001 TYR B 204 ARG 0.002 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8037 (tmt90) outliers start: 15 outliers final: 13 residues processed: 64 average time/residue: 1.5821 time to fit residues: 109.1763 Evaluate side-chains 62 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 508 CYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 429 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 74 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 65 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.094025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.061421 restraints weight = 23624.353| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.64 r_work: 0.2702 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8462 Z= 0.226 Angle : 0.495 10.017 11463 Z= 0.256 Chirality : 0.043 0.196 1252 Planarity : 0.003 0.025 1519 Dihedral : 4.586 51.660 1167 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.09 % Allowed : 13.72 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1069 helix: 0.39 (0.51), residues: 111 sheet: 0.70 (0.28), residues: 337 loop : -0.15 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 51 HIS 0.003 0.000 HIS B 281 PHE 0.009 0.001 PHE B 274 TYR 0.014 0.001 TYR B 204 ARG 0.002 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8030 (tmt90) REVERT: A 547 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8512 (mpt180) REVERT: B 40 GLN cc_start: 0.9078 (tp40) cc_final: 0.8842 (tm-30) outliers start: 19 outliers final: 14 residues processed: 66 average time/residue: 1.5162 time to fit residues: 107.4733 Evaluate side-chains 66 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 508 CYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 432 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 69 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 100 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.094636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.061839 restraints weight = 23622.828| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.66 r_work: 0.2692 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8462 Z= 0.185 Angle : 0.488 13.318 11463 Z= 0.252 Chirality : 0.043 0.240 1252 Planarity : 0.003 0.024 1519 Dihedral : 4.448 50.905 1167 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.87 % Allowed : 13.83 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1069 helix: 0.58 (0.52), residues: 111 sheet: 0.74 (0.28), residues: 338 loop : -0.12 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 51 HIS 0.002 0.000 HIS B 281 PHE 0.009 0.001 PHE B 274 TYR 0.014 0.001 TYR B 204 ARG 0.002 0.000 ARG B 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8038 (tmt90) REVERT: A 563 MET cc_start: 0.8518 (ttt) cc_final: 0.7907 (tpt) REVERT: B 40 GLN cc_start: 0.9108 (tp40) cc_final: 0.8816 (tm-30) outliers start: 17 outliers final: 13 residues processed: 67 average time/residue: 1.5641 time to fit residues: 112.2435 Evaluate side-chains 64 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 508 CYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 432 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 77 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.094590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.062000 restraints weight = 23664.084| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.65 r_work: 0.2696 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8462 Z= 0.189 Angle : 0.493 12.525 11463 Z= 0.255 Chirality : 0.043 0.221 1252 Planarity : 0.003 0.024 1519 Dihedral : 4.153 50.081 1165 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.54 % Allowed : 14.38 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1069 helix: 0.56 (0.52), residues: 111 sheet: 0.77 (0.29), residues: 337 loop : -0.06 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 51 HIS 0.002 0.000 HIS B 281 PHE 0.009 0.001 PHE B 274 TYR 0.014 0.001 TYR B 204 ARG 0.002 0.000 ARG B 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7125.74 seconds wall clock time: 126 minutes 47.90 seconds (7607.90 seconds total)