Starting phenix.real_space_refine on Fri Jul 19 02:08:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgj_41238/07_2024/8tgj_41238_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgj_41238/07_2024/8tgj_41238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgj_41238/07_2024/8tgj_41238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgj_41238/07_2024/8tgj_41238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgj_41238/07_2024/8tgj_41238_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgj_41238/07_2024/8tgj_41238_trim.cif" } resolution = 3.5 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 3805 2.51 5 N 892 2.21 5 O 966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 5720 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2837 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 23, 'TRANS': 357} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2839 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 21, 'TRANS': 358} Chain breaks: 2 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.62, per 1000 atoms: 0.81 Number of scatterers: 5720 At special positions: 0 Unit cell: (74.26, 56.4, 115.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 966 8.00 N 892 7.00 C 3805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.0 seconds 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 90.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 24 through 41 removed outlier: 3.785A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 50 removed outlier: 3.603A pdb=" N PHE A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.877A pdb=" N LEU A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 154 Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 158 through 159 No H-bonds generated for 'chain 'A' and resid 158 through 159' Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 166 through 187 Processing helix chain 'A' and resid 189 through 219 removed outlier: 3.943A pdb=" N VAL A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 254 removed outlier: 4.602A pdb=" N ALA A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 256 through 278 removed outlier: 4.302A pdb=" N PHE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.686A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 331 removed outlier: 3.789A pdb=" N LEU A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Proline residue: A 321 - end of helix Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 337 through 364 removed outlier: 3.956A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Proline residue: A 344 - end of helix removed outlier: 4.109A pdb=" N GLY A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 421 Proline residue: A 412 - end of helix removed outlier: 3.991A pdb=" N GLY A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 455 removed outlier: 4.207A pdb=" N GLY A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 4.942A pdb=" N GLY A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 473 through 480 removed outlier: 4.167A pdb=" N SER A 480 " --> pdb=" O TYR A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 41 removed outlier: 3.955A pdb=" N VAL B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 130 through 134 removed outlier: 4.048A pdb=" N GLU B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 164 removed outlier: 4.554A pdb=" N LYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Proline residue: B 155 - end of helix removed outlier: 4.502A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 166 through 187 Processing helix chain 'B' and resid 189 through 219 removed outlier: 3.662A pdb=" N LEU B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B 194 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 195 " --> pdb=" O THR B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 251 removed outlier: 4.168A pdb=" N ARG B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Proline residue: B 245 - end of helix removed outlier: 3.749A pdb=" N SER B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 276 removed outlier: 4.669A pdb=" N PHE B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 299 through 331 removed outlier: 3.504A pdb=" N ALA B 305 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Proline residue: B 321 - end of helix Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.793A pdb=" N PHE B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 364 removed outlier: 3.750A pdb=" N TYR B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASN B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 388 through 391 Processing helix chain 'B' and resid 392 through 422 removed outlier: 3.651A pdb=" N MET B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Proline residue: B 412 - end of helix removed outlier: 3.670A pdb=" N ARG B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 455 Proline residue: B 445 - end of helix removed outlier: 3.670A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 472 removed outlier: 3.709A pdb=" N LEU B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.551A pdb=" N TYR B 477 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B 479 " --> pdb=" O TYR B 476 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 849 1.31 - 1.43: 1551 1.43 - 1.56: 3360 1.56 - 1.69: 3 1.69 - 1.81: 100 Bond restraints: 5863 Sorted by residual: bond pdb=" C31 YHR B 601 " pdb=" O30 YHR B 601 " ideal model delta sigma weight residual 1.326 1.404 -0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C17 YHR B 601 " pdb=" O19 YHR B 601 " ideal model delta sigma weight residual 1.325 1.397 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C37 YHR B 601 " pdb=" O39 YHR B 601 " ideal model delta sigma weight residual 1.342 1.409 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C13 YHR B 601 " pdb=" N8 YHR B 601 " ideal model delta sigma weight residual 1.459 1.522 -0.063 2.00e-02 2.50e+03 9.92e+00 bond pdb=" C10 YHR B 601 " pdb=" C11 YHR B 601 " ideal model delta sigma weight residual 1.492 1.432 0.060 2.00e-02 2.50e+03 9.15e+00 ... (remaining 5858 not shown) Histogram of bond angle deviations from ideal: 98.75 - 106.28: 216 106.28 - 113.81: 3329 113.81 - 121.34: 3304 121.34 - 128.87: 1102 128.87 - 136.39: 36 Bond angle restraints: 7987 Sorted by residual: angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 111.89 130.18 -18.29 3.00e+00 1.11e-01 3.72e+01 angle pdb=" C ARG B 479 " pdb=" N SER B 480 " pdb=" CA SER B 480 " ideal model delta sigma weight residual 122.83 128.17 -5.34 1.08e+00 8.57e-01 2.44e+01 angle pdb=" CA ASN A 388 " pdb=" CB ASN A 388 " pdb=" CG ASN A 388 " ideal model delta sigma weight residual 112.60 116.89 -4.29 1.00e+00 1.00e+00 1.84e+01 angle pdb=" N LEU A 24 " pdb=" CA LEU A 24 " pdb=" C LEU A 24 " ideal model delta sigma weight residual 110.80 102.06 8.74 2.13e+00 2.20e-01 1.68e+01 angle pdb=" CA ILE A 463 " pdb=" CB ILE A 463 " pdb=" CG1 ILE A 463 " ideal model delta sigma weight residual 110.40 116.95 -6.55 1.70e+00 3.46e-01 1.48e+01 ... (remaining 7982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.61: 3030 22.61 - 45.23: 356 45.23 - 67.84: 47 67.84 - 90.45: 8 90.45 - 113.07: 1 Dihedral angle restraints: 3442 sinusoidal: 1306 harmonic: 2136 Sorted by residual: dihedral pdb=" C13 YHR B 601 " pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C6 YHR B 601 " ideal model delta sinusoidal sigma weight residual 57.66 -55.41 113.07 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" CA VAL B 358 " pdb=" C VAL B 358 " pdb=" N LEU B 359 " pdb=" CA LEU B 359 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE B 356 " pdb=" C PHE B 356 " pdb=" N GLY B 357 " pdb=" CA GLY B 357 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 3439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 892 0.082 - 0.164: 62 0.164 - 0.246: 6 0.246 - 0.328: 0 0.328 - 0.410: 1 Chirality restraints: 961 Sorted by residual: chirality pdb=" C13 YHR B 601 " pdb=" C12 YHR B 601 " pdb=" C14 YHR B 601 " pdb=" N8 YHR B 601 " both_signs ideal model delta sigma weight residual False -2.29 -2.70 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CA LEU A 24 " pdb=" N LEU A 24 " pdb=" C LEU A 24 " pdb=" CB LEU A 24 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA MET B 331 " pdb=" N MET B 331 " pdb=" C MET B 331 " pdb=" CB MET B 331 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.54e-01 ... (remaining 958 not shown) Planarity restraints: 972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 472 " -0.079 5.00e-02 4.00e+02 1.18e-01 2.21e+01 pdb=" N PRO B 473 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO B 473 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 473 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 471 " 0.013 2.00e-02 2.50e+03 1.76e-02 6.18e+00 pdb=" CG TYR A 471 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 471 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 471 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 471 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 471 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 471 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 471 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 158 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO B 159 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 159 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 159 " 0.033 5.00e-02 4.00e+02 ... (remaining 969 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1674 2.81 - 3.34: 5837 3.34 - 3.86: 9548 3.86 - 4.38: 10360 4.38 - 4.90: 18819 Nonbonded interactions: 46238 Sorted by model distance: nonbonded pdb=" OE1 GLU B 135 " pdb=" NH1 ARG B 138 " model vdw 2.292 2.520 nonbonded pdb=" O PHE A 143 " pdb=" NH2 ARG A 197 " model vdw 2.339 2.520 nonbonded pdb=" O VAL A 375 " pdb=" OG SER A 379 " model vdw 2.343 2.440 nonbonded pdb=" O SER A 284 " pdb=" OG SER A 284 " model vdw 2.373 2.440 nonbonded pdb=" OD1 ASN A 154 " pdb=" OG SER A 205 " model vdw 2.422 2.440 ... (remaining 46233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 278 or resid 289 through 482)) selection = (chain 'B' and ((resid 19 and (name CA or name C or name O or name CB or name OG \ )) or resid 20 through 50 or resid 136 through 482)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.890 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 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 0.078 5863 Z= 0.286 Angle : 0.780 18.286 7987 Z= 0.395 Chirality : 0.045 0.410 961 Planarity : 0.008 0.118 972 Dihedral : 18.014 113.067 2086 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 25.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.66 % Allowed : 34.59 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.30), residues: 751 helix: 0.87 (0.21), residues: 593 sheet: None (None), residues: 0 loop : -1.26 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 336 HIS 0.003 0.001 HIS A 223 PHE 0.036 0.001 PHE B 28 TYR 0.043 0.002 TYR A 471 ARG 0.003 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 159 time to evaluate : 0.599 Fit side-chains REVERT: A 190 TYR cc_start: 0.6527 (t80) cc_final: 0.5808 (t80) REVERT: A 194 PHE cc_start: 0.8027 (t80) cc_final: 0.7420 (m-80) REVERT: A 268 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7767 (mp) REVERT: B 439 MET cc_start: 0.7454 (tpp) cc_final: 0.7215 (mmm) outliers start: 4 outliers final: 1 residues processed: 161 average time/residue: 0.1315 time to fit residues: 29.6005 Evaluate side-chains 163 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 36 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.0770 chunk 23 optimal weight: 0.0270 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.0170 chunk 69 optimal weight: 0.7980 overall best weight: 0.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN B 329 GLN B 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5863 Z= 0.193 Angle : 0.654 9.139 7987 Z= 0.314 Chirality : 0.042 0.140 961 Planarity : 0.006 0.056 972 Dihedral : 5.780 47.374 868 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.75 % Allowed : 30.49 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.31), residues: 751 helix: 1.44 (0.21), residues: 607 sheet: None (None), residues: 0 loop : -1.25 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 336 HIS 0.001 0.000 HIS B 167 PHE 0.017 0.001 PHE B 356 TYR 0.018 0.001 TYR A 471 ARG 0.002 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 467 ILE cc_start: 0.7793 (tt) cc_final: 0.7501 (tp) REVERT: A 471 TYR cc_start: 0.7873 (t80) cc_final: 0.7171 (t80) REVERT: B 373 MET cc_start: 0.7573 (mtp) cc_final: 0.7281 (mmm) REVERT: B 439 MET cc_start: 0.7408 (tpp) cc_final: 0.7154 (mmm) REVERT: B 461 MET cc_start: 0.6858 (mmm) cc_final: 0.6469 (mmt) outliers start: 29 outliers final: 15 residues processed: 180 average time/residue: 0.1368 time to fit residues: 34.1164 Evaluate side-chains 176 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 0.1980 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 68 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5863 Z= 0.232 Angle : 0.648 8.238 7987 Z= 0.312 Chirality : 0.043 0.139 961 Planarity : 0.005 0.062 972 Dihedral : 4.800 42.416 863 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.08 % Allowed : 30.82 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.32), residues: 751 helix: 1.50 (0.22), residues: 614 sheet: None (None), residues: 0 loop : -1.76 (0.48), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 326 HIS 0.002 0.001 HIS A 422 PHE 0.022 0.001 PHE A 253 TYR 0.012 0.001 TYR A 430 ARG 0.002 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7365 (tt0) cc_final: 0.7129 (tt0) REVERT: A 249 VAL cc_start: 0.7914 (m) cc_final: 0.7475 (p) REVERT: A 253 PHE cc_start: 0.7033 (m-80) cc_final: 0.6815 (m-80) REVERT: A 467 ILE cc_start: 0.7876 (tt) cc_final: 0.7571 (tp) REVERT: A 471 TYR cc_start: 0.7944 (t80) cc_final: 0.7037 (t80) REVERT: B 170 MET cc_start: 0.7022 (tpp) cc_final: 0.6607 (tpp) REVERT: B 331 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7246 (mtm) REVERT: B 439 MET cc_start: 0.7394 (tpp) cc_final: 0.7090 (mmm) REVERT: B 452 VAL cc_start: 0.7444 (m) cc_final: 0.7113 (p) REVERT: B 461 MET cc_start: 0.6902 (mmm) cc_final: 0.6470 (mmt) REVERT: B 480 SER cc_start: 0.7458 (t) cc_final: 0.7179 (p) outliers start: 31 outliers final: 20 residues processed: 177 average time/residue: 0.1335 time to fit residues: 32.9379 Evaluate side-chains 179 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.9990 chunk 51 optimal weight: 0.0970 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.2980 chunk 36 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5863 Z= 0.215 Angle : 0.633 7.632 7987 Z= 0.305 Chirality : 0.042 0.136 961 Planarity : 0.005 0.063 972 Dihedral : 4.711 43.007 863 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.74 % Allowed : 30.49 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.32), residues: 751 helix: 1.55 (0.22), residues: 615 sheet: None (None), residues: 0 loop : -1.77 (0.47), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.002 0.001 HIS A 387 PHE 0.017 0.001 PHE B 356 TYR 0.014 0.001 TYR A 430 ARG 0.002 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7366 (tt0) cc_final: 0.7100 (tt0) REVERT: A 149 MET cc_start: 0.7033 (tpp) cc_final: 0.6745 (tpp) REVERT: A 249 VAL cc_start: 0.7870 (m) cc_final: 0.7293 (p) REVERT: A 253 PHE cc_start: 0.7064 (m-80) cc_final: 0.6796 (m-80) REVERT: A 439 MET cc_start: 0.6340 (OUTLIER) cc_final: 0.6051 (ttp) REVERT: A 463 ILE cc_start: 0.7553 (mt) cc_final: 0.7138 (mm) REVERT: A 467 ILE cc_start: 0.7884 (tt) cc_final: 0.7564 (tp) REVERT: A 471 TYR cc_start: 0.8038 (t80) cc_final: 0.7338 (t80) REVERT: A 474 LEU cc_start: 0.7848 (mt) cc_final: 0.7526 (mp) REVERT: B 331 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7120 (mtm) REVERT: B 439 MET cc_start: 0.7362 (tpp) cc_final: 0.7035 (mmm) REVERT: B 452 VAL cc_start: 0.7419 (m) cc_final: 0.7118 (p) REVERT: B 461 MET cc_start: 0.6866 (mmm) cc_final: 0.6459 (mmt) REVERT: B 480 SER cc_start: 0.7463 (t) cc_final: 0.7167 (p) outliers start: 35 outliers final: 20 residues processed: 181 average time/residue: 0.1315 time to fit residues: 33.1521 Evaluate side-chains 185 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 163 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 62 optimal weight: 0.0770 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5863 Z= 0.240 Angle : 0.650 8.235 7987 Z= 0.311 Chirality : 0.042 0.140 961 Planarity : 0.005 0.064 972 Dihedral : 4.652 43.047 863 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 6.89 % Allowed : 29.51 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.31), residues: 751 helix: 1.55 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -1.62 (0.45), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 326 HIS 0.001 0.001 HIS A 422 PHE 0.017 0.001 PHE B 356 TYR 0.013 0.001 TYR A 430 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 166 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7377 (tt0) cc_final: 0.7110 (tt0) REVERT: A 149 MET cc_start: 0.7087 (tpp) cc_final: 0.6781 (tpp) REVERT: A 249 VAL cc_start: 0.7868 (m) cc_final: 0.6975 (p) REVERT: A 250 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.6803 (mpp) REVERT: A 253 PHE cc_start: 0.7105 (m-80) cc_final: 0.6848 (m-80) REVERT: A 467 ILE cc_start: 0.7916 (tt) cc_final: 0.7632 (tp) REVERT: A 471 TYR cc_start: 0.8074 (t80) cc_final: 0.7397 (t80) REVERT: B 135 GLU cc_start: 0.5914 (OUTLIER) cc_final: 0.5661 (mm-30) REVERT: B 170 MET cc_start: 0.6969 (tpp) cc_final: 0.6388 (tpp) REVERT: B 439 MET cc_start: 0.7348 (tpp) cc_final: 0.7025 (mmm) REVERT: B 452 VAL cc_start: 0.7424 (m) cc_final: 0.7151 (p) REVERT: B 480 SER cc_start: 0.7542 (t) cc_final: 0.7226 (p) outliers start: 42 outliers final: 27 residues processed: 185 average time/residue: 0.1249 time to fit residues: 32.2971 Evaluate side-chains 192 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 61 optimal weight: 0.0000 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 overall best weight: 0.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS B 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5863 Z= 0.200 Angle : 0.646 7.710 7987 Z= 0.306 Chirality : 0.042 0.179 961 Planarity : 0.005 0.063 972 Dihedral : 4.618 41.992 863 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 6.23 % Allowed : 30.66 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.31), residues: 751 helix: 1.58 (0.22), residues: 616 sheet: None (None), residues: 0 loop : -1.57 (0.47), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.001 0.000 HIS A 223 PHE 0.017 0.001 PHE B 356 TYR 0.011 0.001 TYR A 430 ARG 0.002 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 172 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7354 (tt0) cc_final: 0.7094 (tt0) REVERT: A 149 MET cc_start: 0.7081 (tpp) cc_final: 0.6755 (tpp) REVERT: A 249 VAL cc_start: 0.7828 (m) cc_final: 0.6919 (p) REVERT: A 250 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.6813 (mpp) REVERT: A 253 PHE cc_start: 0.7105 (m-80) cc_final: 0.6891 (m-80) REVERT: A 374 LEU cc_start: 0.8397 (mt) cc_final: 0.8112 (mt) REVERT: A 463 ILE cc_start: 0.7495 (mt) cc_final: 0.7013 (mm) REVERT: A 467 ILE cc_start: 0.7922 (tt) cc_final: 0.7606 (tp) REVERT: A 471 TYR cc_start: 0.8094 (t80) cc_final: 0.7232 (t80) REVERT: A 474 LEU cc_start: 0.7870 (mt) cc_final: 0.7533 (mp) REVERT: B 135 GLU cc_start: 0.5861 (OUTLIER) cc_final: 0.5623 (mm-30) REVERT: B 439 MET cc_start: 0.7315 (tpp) cc_final: 0.7006 (mmm) REVERT: B 452 VAL cc_start: 0.7442 (m) cc_final: 0.7191 (p) REVERT: B 480 SER cc_start: 0.7534 (t) cc_final: 0.7215 (p) outliers start: 38 outliers final: 24 residues processed: 192 average time/residue: 0.1282 time to fit residues: 34.3273 Evaluate side-chains 194 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 45 optimal weight: 0.0970 chunk 44 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN B 396 ASN B 468 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5863 Z= 0.250 Angle : 0.665 7.266 7987 Z= 0.320 Chirality : 0.043 0.146 961 Planarity : 0.005 0.064 972 Dihedral : 4.610 42.471 863 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.57 % Allowed : 31.15 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.31), residues: 751 helix: 1.56 (0.22), residues: 610 sheet: None (None), residues: 0 loop : -1.50 (0.46), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 366 HIS 0.003 0.001 HIS B 167 PHE 0.017 0.001 PHE B 356 TYR 0.012 0.001 TYR A 430 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 166 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7377 (tt0) cc_final: 0.7128 (tt0) REVERT: A 149 MET cc_start: 0.7154 (tpp) cc_final: 0.6845 (tpp) REVERT: A 249 VAL cc_start: 0.7864 (m) cc_final: 0.6929 (p) REVERT: A 250 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.6856 (mpp) REVERT: A 253 PHE cc_start: 0.7110 (m-80) cc_final: 0.6889 (m-80) REVERT: A 463 ILE cc_start: 0.7497 (mt) cc_final: 0.7067 (mm) REVERT: A 471 TYR cc_start: 0.8137 (t80) cc_final: 0.7200 (t80) REVERT: A 474 LEU cc_start: 0.7888 (mt) cc_final: 0.7553 (mp) REVERT: B 135 GLU cc_start: 0.5930 (OUTLIER) cc_final: 0.5671 (mm-30) REVERT: B 148 VAL cc_start: 0.7325 (p) cc_final: 0.7003 (m) REVERT: B 170 MET cc_start: 0.7016 (tpp) cc_final: 0.6326 (tpp) REVERT: B 331 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7479 (mtm) REVERT: B 452 VAL cc_start: 0.7456 (m) cc_final: 0.7207 (p) REVERT: B 480 SER cc_start: 0.7647 (t) cc_final: 0.7340 (p) outliers start: 34 outliers final: 24 residues processed: 182 average time/residue: 0.1251 time to fit residues: 32.0519 Evaluate side-chains 189 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.0010 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 0.0270 chunk 70 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5863 Z= 0.225 Angle : 0.674 12.273 7987 Z= 0.318 Chirality : 0.042 0.139 961 Planarity : 0.005 0.064 972 Dihedral : 4.677 43.161 863 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.90 % Allowed : 30.98 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.31), residues: 751 helix: 1.59 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -1.52 (0.45), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 336 HIS 0.001 0.000 HIS B 167 PHE 0.028 0.001 PHE B 28 TYR 0.012 0.001 TYR A 430 ARG 0.002 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7356 (tt0) cc_final: 0.7104 (tt0) REVERT: A 149 MET cc_start: 0.7100 (tpp) cc_final: 0.6783 (tpp) REVERT: A 249 VAL cc_start: 0.7846 (m) cc_final: 0.6874 (p) REVERT: A 250 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.6803 (mpp) REVERT: A 253 PHE cc_start: 0.7102 (m-80) cc_final: 0.6874 (m-80) REVERT: A 471 TYR cc_start: 0.8122 (t80) cc_final: 0.7259 (t80) REVERT: A 474 LEU cc_start: 0.7874 (mt) cc_final: 0.7534 (mp) REVERT: B 135 GLU cc_start: 0.5897 (OUTLIER) cc_final: 0.5661 (mm-30) REVERT: B 331 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7204 (mtm) REVERT: B 452 VAL cc_start: 0.7425 (m) cc_final: 0.7168 (p) REVERT: B 461 MET cc_start: 0.6835 (mmm) cc_final: 0.6558 (mmt) REVERT: B 480 SER cc_start: 0.7612 (t) cc_final: 0.7305 (p) outliers start: 36 outliers final: 24 residues processed: 182 average time/residue: 0.1288 time to fit residues: 32.8067 Evaluate side-chains 190 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 163 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 50 optimal weight: 0.0050 chunk 75 optimal weight: 0.5980 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5863 Z= 0.214 Angle : 0.671 10.619 7987 Z= 0.317 Chirality : 0.043 0.158 961 Planarity : 0.005 0.063 972 Dihedral : 4.667 43.024 863 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.57 % Allowed : 31.15 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.31), residues: 751 helix: 1.60 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -1.42 (0.46), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 336 HIS 0.001 0.000 HIS A 387 PHE 0.017 0.001 PHE B 356 TYR 0.011 0.001 TYR A 430 ARG 0.004 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 162 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8429 (tp) cc_final: 0.8156 (tt) REVERT: A 149 MET cc_start: 0.7099 (tpp) cc_final: 0.6800 (tpp) REVERT: A 249 VAL cc_start: 0.7806 (m) cc_final: 0.6978 (p) REVERT: A 250 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.6826 (mpp) REVERT: A 253 PHE cc_start: 0.7099 (m-80) cc_final: 0.6883 (m-80) REVERT: A 471 TYR cc_start: 0.8021 (t80) cc_final: 0.7152 (t80) REVERT: A 474 LEU cc_start: 0.7840 (mt) cc_final: 0.7504 (mp) REVERT: B 135 GLU cc_start: 0.5868 (OUTLIER) cc_final: 0.5621 (mm-30) REVERT: B 331 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.6980 (mtm) REVERT: B 439 MET cc_start: 0.7337 (tpp) cc_final: 0.7103 (mmm) REVERT: B 452 VAL cc_start: 0.7439 (m) cc_final: 0.7190 (p) REVERT: B 461 MET cc_start: 0.6795 (mmm) cc_final: 0.6532 (mmt) REVERT: B 480 SER cc_start: 0.7642 (t) cc_final: 0.7343 (p) outliers start: 34 outliers final: 27 residues processed: 178 average time/residue: 0.1232 time to fit residues: 31.1334 Evaluate side-chains 191 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 0.0270 chunk 47 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN B 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5863 Z= 0.240 Angle : 0.681 10.312 7987 Z= 0.324 Chirality : 0.043 0.174 961 Planarity : 0.005 0.064 972 Dihedral : 4.675 43.583 863 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.08 % Allowed : 31.31 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.31), residues: 751 helix: 1.55 (0.22), residues: 610 sheet: None (None), residues: 0 loop : -1.24 (0.47), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 366 HIS 0.001 0.001 HIS B 167 PHE 0.017 0.001 PHE A 356 TYR 0.013 0.001 TYR A 430 ARG 0.003 0.000 ARG B 479 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 162 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8433 (tp) cc_final: 0.8177 (tt) REVERT: A 149 MET cc_start: 0.7149 (tpp) cc_final: 0.6853 (tpp) REVERT: A 249 VAL cc_start: 0.7839 (m) cc_final: 0.6935 (p) REVERT: A 250 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.6809 (mpp) REVERT: A 253 PHE cc_start: 0.7101 (m-80) cc_final: 0.6878 (m-80) REVERT: A 471 TYR cc_start: 0.7985 (t80) cc_final: 0.7422 (t80) REVERT: A 474 LEU cc_start: 0.7899 (mt) cc_final: 0.7546 (mp) REVERT: B 135 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5627 (mm-30) REVERT: B 331 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.6941 (mtm) REVERT: B 439 MET cc_start: 0.7347 (tpp) cc_final: 0.7110 (mmm) REVERT: B 452 VAL cc_start: 0.7451 (m) cc_final: 0.7219 (p) REVERT: B 480 SER cc_start: 0.7724 (t) cc_final: 0.7478 (p) outliers start: 31 outliers final: 26 residues processed: 175 average time/residue: 0.1240 time to fit residues: 30.8488 Evaluate side-chains 189 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 3 optimal weight: 0.0370 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.139522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.126296 restraints weight = 8849.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.130194 restraints weight = 4430.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.132676 restraints weight = 2552.001| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5863 Z= 0.215 Angle : 0.672 10.100 7987 Z= 0.319 Chirality : 0.043 0.172 961 Planarity : 0.005 0.063 972 Dihedral : 4.674 43.070 863 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.41 % Allowed : 31.31 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.31), residues: 751 helix: 1.60 (0.22), residues: 607 sheet: None (None), residues: 0 loop : -1.42 (0.46), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 336 HIS 0.002 0.000 HIS B 167 PHE 0.017 0.001 PHE B 356 TYR 0.014 0.001 TYR A 430 ARG 0.003 0.000 ARG B 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1542.36 seconds wall clock time: 28 minutes 2.41 seconds (1682.41 seconds total)