Starting phenix.real_space_refine on Sun Apr 27 13:04:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tgj_41238/04_2025/8tgj_41238_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tgj_41238/04_2025/8tgj_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/cci-nas-00/data/ceres_data/8tgj_41238/04_2025/8tgj_41238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tgj_41238/04_2025/8tgj_41238.map" model { file = "/net/cci-nas-00/data/ceres_data/8tgj_41238/04_2025/8tgj_41238_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tgj_41238/04_2025/8tgj_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. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 4.26, per 1000 atoms: 0.74 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 - 3.00 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: 1.42 Conformation dependent library (CDL) restraints added in 860.2 milliseconds 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: 0.60 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: 1.70 Time building geometry restraints manager: 1.65 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: 0.00 - 3.66: 7923 3.66 - 7.31: 55 7.31 - 10.97: 8 10.97 - 14.63: 0 14.63 - 18.29: 1 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 3.120 nonbonded pdb=" O PHE A 143 " pdb=" NH2 ARG A 197 " model vdw 2.339 3.120 nonbonded pdb=" O VAL A 375 " pdb=" OG SER A 379 " model vdw 2.343 3.040 nonbonded pdb=" O SER A 284 " pdb=" OG SER A 284 " model vdw 2.373 3.040 nonbonded pdb=" OD1 ASN A 154 " pdb=" OG SER A 205 " model vdw 2.422 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.780 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.480 ------------------------------------------------------------------------------- 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= 0.219 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 Details of bonding type rmsd hydrogen bonds : bond 0.15863 ( 450) hydrogen bonds : angle 5.58577 ( 1323) covalent geometry : bond 0.00434 ( 5863) covalent geometry : angle 0.78011 ( 7987) *********************** 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 to be fit. rotamer outliers: 4 poor density : 159 time to evaluate : 0.608 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: 0.1346 time to fit residues: 30.3800 Evaluate side-chains 163 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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: 0.5980 chunk 57 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 38 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.0170 chunk 23 optimal weight: 0.0030 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 69 optimal weight: 0.5980 overall best weight: 0.1428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.143961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.131272 restraints weight = 8766.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.135102 restraints weight = 4387.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.137488 restraints weight = 2496.064| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5863 Z= 0.138 Angle : 0.660 9.111 7987 Z= 0.317 Chirality : 0.042 0.137 961 Planarity : 0.006 0.055 972 Dihedral : 5.770 47.494 868 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.59 % Allowed : 29.84 % Favored : 65.57 % 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: 1.35 (0.31), residues: 751 helix: 1.42 (0.22), residues: 607 sheet: None (None), residues: 0 loop : -1.25 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 336 HIS 0.001 0.000 HIS A 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 Details of bonding type rmsd hydrogen bonds : bond 0.04274 ( 450) hydrogen bonds : angle 4.25856 ( 1323) covalent geometry : bond 0.00291 ( 5863) covalent geometry : angle 0.66000 ( 7987) *********************** 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 200 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 249 VAL cc_start: 0.7872 (m) cc_final: 0.7506 (p) REVERT: A 467 ILE cc_start: 0.7833 (tt) cc_final: 0.7541 (tp) REVERT: A 471 TYR cc_start: 0.8306 (t80) cc_final: 0.8079 (t80) REVERT: A 474 LEU cc_start: 0.7812 (mt) cc_final: 0.7478 (mp) REVERT: B 373 MET cc_start: 0.7461 (mtp) cc_final: 0.7161 (mmm) REVERT: B 461 MET cc_start: 0.6756 (mmm) cc_final: 0.6322 (mmt) outliers start: 28 outliers final: 14 residues processed: 184 average time/residue: 0.1298 time to fit residues: 33.1970 Evaluate side-chains 179 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 229 MET Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 346 SER 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 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 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 75 optimal weight: 0.0020 chunk 22 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 60 optimal weight: 0.0170 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 overall best weight: 0.3426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 337 GLN B 468 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.142624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.130187 restraints weight = 8735.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.133954 restraints weight = 4316.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.136376 restraints weight = 2442.051| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5863 Z= 0.144 Angle : 0.653 8.346 7987 Z= 0.311 Chirality : 0.043 0.189 961 Planarity : 0.005 0.062 972 Dihedral : 4.793 41.901 863 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.59 % Allowed : 31.64 % 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: 1.56 (0.32), residues: 751 helix: 1.60 (0.22), residues: 607 sheet: None (None), residues: 0 loop : -1.32 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 326 HIS 0.001 0.000 HIS A 422 PHE 0.024 0.001 PHE A 253 TYR 0.014 0.001 TYR A 471 ARG 0.002 0.000 ARG B 421 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 450) hydrogen bonds : angle 4.14948 ( 1323) covalent geometry : bond 0.00333 ( 5863) covalent geometry : angle 0.65294 ( 7987) *********************** 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 196 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7338 (tt0) cc_final: 0.7100 (tt0) REVERT: A 249 VAL cc_start: 0.7829 (m) cc_final: 0.7433 (p) REVERT: A 299 ASP cc_start: 0.7338 (t0) cc_final: 0.7088 (m-30) REVERT: A 463 ILE cc_start: 0.7583 (mt) cc_final: 0.7123 (mp) REVERT: A 467 ILE cc_start: 0.7951 (tt) cc_final: 0.7631 (tp) REVERT: A 474 LEU cc_start: 0.7851 (mt) cc_final: 0.7532 (mp) REVERT: B 170 MET cc_start: 0.7070 (tpp) cc_final: 0.6708 (tpp) REVERT: B 331 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7276 (mtm) REVERT: B 373 MET cc_start: 0.7411 (mtp) cc_final: 0.7156 (mmm) REVERT: B 452 VAL cc_start: 0.7340 (m) cc_final: 0.6998 (p) REVERT: B 461 MET cc_start: 0.6779 (mmm) cc_final: 0.6424 (mmt) outliers start: 28 outliers final: 15 residues processed: 182 average time/residue: 0.1367 time to fit residues: 34.7965 Evaluate side-chains 177 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 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 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 439 MET 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 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 47 optimal weight: 0.0170 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.139423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.126297 restraints weight = 9034.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.130201 restraints weight = 4483.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.132699 restraints weight = 2554.906| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5863 Z= 0.184 Angle : 0.665 8.227 7987 Z= 0.323 Chirality : 0.044 0.140 961 Planarity : 0.005 0.065 972 Dihedral : 4.754 43.464 863 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 6.23 % Allowed : 29.67 % 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: 1.40 (0.31), residues: 751 helix: 1.54 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -1.64 (0.46), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.002 0.001 HIS B 387 PHE 0.026 0.001 PHE A 253 TYR 0.015 0.001 TYR A 430 ARG 0.002 0.000 ARG B 225 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 450) hydrogen bonds : angle 4.16968 ( 1323) covalent geometry : bond 0.00422 ( 5863) covalent geometry : angle 0.66469 ( 7987) *********************** 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 203 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7405 (tt0) cc_final: 0.7142 (tt0) REVERT: A 150 GLN cc_start: 0.6947 (tt0) cc_final: 0.6704 (tt0) REVERT: A 249 VAL cc_start: 0.7817 (m) cc_final: 0.7370 (p) REVERT: A 250 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.6789 (mpp) REVERT: A 299 ASP cc_start: 0.7401 (t0) cc_final: 0.7168 (m-30) REVERT: A 463 ILE cc_start: 0.7633 (mt) cc_final: 0.7310 (mm) REVERT: A 474 LEU cc_start: 0.7878 (mt) cc_final: 0.7544 (mp) REVERT: B 331 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7185 (mtm) REVERT: B 452 VAL cc_start: 0.7388 (m) cc_final: 0.7090 (p) outliers start: 38 outliers final: 19 residues processed: 181 average time/residue: 0.1701 time to fit residues: 42.7540 Evaluate side-chains 190 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 184 PHE 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 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 194 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 387 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 35 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.140202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.127740 restraints weight = 8706.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.131518 restraints weight = 4316.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.133900 restraints weight = 2448.473| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1872 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= 0.159 Angle : 0.660 8.197 7987 Z= 0.316 Chirality : 0.043 0.139 961 Planarity : 0.005 0.066 972 Dihedral : 4.718 44.279 863 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.57 % Allowed : 30.16 % Favored : 64.26 % 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 (0.31), residues: 751 helix: 1.51 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -1.64 (0.46), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.001 0.000 HIS A 422 PHE 0.021 0.001 PHE A 253 TYR 0.014 0.001 TYR A 430 ARG 0.001 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 450) hydrogen bonds : angle 4.16396 ( 1323) covalent geometry : bond 0.00366 ( 5863) covalent geometry : angle 0.65997 ( 7987) *********************** 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 203 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7346 (tt0) cc_final: 0.7099 (tt0) REVERT: A 249 VAL cc_start: 0.7796 (m) cc_final: 0.7132 (p) REVERT: A 250 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.6828 (mpp) REVERT: A 253 PHE cc_start: 0.6996 (m-80) cc_final: 0.6771 (m-80) REVERT: A 299 ASP cc_start: 0.7376 (t0) cc_final: 0.7167 (m-30) REVERT: A 463 ILE cc_start: 0.7615 (mt) cc_final: 0.7185 (mm) REVERT: A 467 ILE cc_start: 0.8020 (tt) cc_final: 0.7796 (tt) REVERT: A 474 LEU cc_start: 0.7856 (mt) cc_final: 0.7519 (mp) REVERT: B 170 MET cc_start: 0.7045 (tpp) cc_final: 0.6531 (tpp) REVERT: B 452 VAL cc_start: 0.7323 (m) cc_final: 0.7051 (p) REVERT: B 480 SER cc_start: 0.7537 (t) cc_final: 0.7174 (p) outliers start: 34 outliers final: 21 residues processed: 184 average time/residue: 0.1284 time to fit residues: 33.1622 Evaluate side-chains 187 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 184 PHE 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 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 194 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 479 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 0.3980 chunk 65 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 0.0070 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.141324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128845 restraints weight = 8761.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.132628 restraints weight = 4325.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.135057 restraints weight = 2445.660| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5863 Z= 0.150 Angle : 0.656 7.327 7987 Z= 0.315 Chirality : 0.043 0.174 961 Planarity : 0.005 0.066 972 Dihedral : 4.698 43.118 863 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.38 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: 1.39 (0.31), residues: 751 helix: 1.51 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -1.59 (0.46), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.001 0.000 HIS A 387 PHE 0.020 0.001 PHE A 253 TYR 0.018 0.001 TYR A 476 ARG 0.001 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 450) hydrogen bonds : angle 4.11587 ( 1323) covalent geometry : bond 0.00345 ( 5863) covalent geometry : angle 0.65601 ( 7987) *********************** 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 203 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7384 (tt0) cc_final: 0.7133 (tt0) REVERT: A 249 VAL cc_start: 0.7777 (m) cc_final: 0.7076 (p) REVERT: A 250 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.6787 (mpp) REVERT: A 253 PHE cc_start: 0.7008 (m-80) cc_final: 0.6777 (m-80) REVERT: A 463 ILE cc_start: 0.7583 (mt) cc_final: 0.7130 (mm) REVERT: A 471 TYR cc_start: 0.8203 (t80) cc_final: 0.7355 (t80) REVERT: A 474 LEU cc_start: 0.7847 (mt) cc_final: 0.7507 (mp) REVERT: A 476 TYR cc_start: 0.8041 (t80) cc_final: 0.7653 (t80) REVERT: B 170 MET cc_start: 0.6968 (tpp) cc_final: 0.6605 (tpp) REVERT: B 452 VAL cc_start: 0.7389 (m) cc_final: 0.7120 (p) REVERT: B 480 SER cc_start: 0.7574 (t) cc_final: 0.7198 (p) outliers start: 35 outliers final: 23 residues processed: 184 average time/residue: 0.1253 time to fit residues: 32.2969 Evaluate side-chains 189 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 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 295 MET 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 405 MET 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 37 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 132 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 274 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 = 0.3842 r_free = 0.3842 target = 0.137330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.124387 restraints weight = 8934.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.128237 restraints weight = 4423.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.130761 restraints weight = 2525.104| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5863 Z= 0.200 Angle : 0.700 11.163 7987 Z= 0.338 Chirality : 0.044 0.180 961 Planarity : 0.006 0.067 972 Dihedral : 4.779 43.458 863 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 6.23 % Allowed : 30.33 % Favored : 63.44 % 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: 1.27 (0.31), residues: 751 helix: 1.37 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -1.36 (0.47), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 366 HIS 0.002 0.001 HIS A 422 PHE 0.018 0.001 PHE A 253 TYR 0.019 0.001 TYR A 476 ARG 0.002 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 450) hydrogen bonds : angle 4.22939 ( 1323) covalent geometry : bond 0.00457 ( 5863) covalent geometry : angle 0.70012 ( 7987) *********************** 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 201 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7414 (tt0) cc_final: 0.7157 (tt0) REVERT: A 249 VAL cc_start: 0.7805 (m) cc_final: 0.7029 (p) REVERT: A 250 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.6859 (mpp) REVERT: A 253 PHE cc_start: 0.7084 (m-80) cc_final: 0.6840 (m-80) REVERT: A 471 TYR cc_start: 0.8187 (t80) cc_final: 0.7308 (t80) REVERT: A 474 LEU cc_start: 0.7859 (mt) cc_final: 0.7526 (mp) REVERT: A 476 TYR cc_start: 0.8100 (t80) cc_final: 0.7669 (t80) REVERT: B 170 MET cc_start: 0.7028 (tpp) cc_final: 0.6569 (tpp) REVERT: B 452 VAL cc_start: 0.7470 (m) cc_final: 0.7200 (p) REVERT: B 480 SER cc_start: 0.7618 (t) cc_final: 0.7239 (p) outliers start: 38 outliers final: 22 residues processed: 181 average time/residue: 0.2015 time to fit residues: 51.7346 Evaluate side-chains 183 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 184 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 205 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 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 405 MET 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 37 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 297 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 5 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 GLN B 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.139078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126250 restraints weight = 8759.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.130096 restraints weight = 4322.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.132573 restraints weight = 2461.044| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5863 Z= 0.172 Angle : 0.696 12.021 7987 Z= 0.333 Chirality : 0.044 0.161 961 Planarity : 0.005 0.067 972 Dihedral : 4.813 42.696 863 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.25 % Allowed : 30.82 % Favored : 63.93 % 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: 1.33 (0.31), residues: 751 helix: 1.41 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -1.36 (0.47), residues: 142 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 0.018 0.001 TYR A 476 ARG 0.002 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 450) hydrogen bonds : angle 4.20417 ( 1323) covalent geometry : bond 0.00395 ( 5863) covalent geometry : angle 0.69649 ( 7987) *********************** 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 190 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7391 (tt0) cc_final: 0.7134 (tt0) REVERT: A 39 THR cc_start: 0.8304 (t) cc_final: 0.8049 (t) REVERT: A 249 VAL cc_start: 0.7779 (m) cc_final: 0.7046 (p) REVERT: A 250 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.6849 (mpp) REVERT: A 253 PHE cc_start: 0.7078 (m-80) cc_final: 0.6835 (m-80) REVERT: A 471 TYR cc_start: 0.8179 (t80) cc_final: 0.7290 (t80) REVERT: A 474 LEU cc_start: 0.7855 (mt) cc_final: 0.7520 (mp) REVERT: A 476 TYR cc_start: 0.8118 (t80) cc_final: 0.7654 (t80) REVERT: B 127 GLN cc_start: 0.5420 (OUTLIER) cc_final: 0.5047 (tm-30) REVERT: B 170 MET cc_start: 0.6926 (tpp) cc_final: 0.6555 (tpp) REVERT: B 452 VAL cc_start: 0.7448 (m) cc_final: 0.7175 (p) REVERT: B 461 MET cc_start: 0.6924 (mmm) cc_final: 0.6546 (mmt) REVERT: B 480 SER cc_start: 0.7665 (t) cc_final: 0.7323 (p) outliers start: 32 outliers final: 22 residues processed: 173 average time/residue: 0.1286 time to fit residues: 31.1425 Evaluate side-chains 182 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL 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 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 405 MET 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 44 ILE Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 132 LEU 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 302 ILE 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 68 optimal weight: 0.0870 chunk 19 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 59 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 62 optimal weight: 0.0980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 ASN ** 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 = 0.3879 r_free = 0.3879 target = 0.140472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.127513 restraints weight = 8916.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.131411 restraints weight = 4398.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.133946 restraints weight = 2499.018| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2230 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= 0.144 Angle : 0.699 10.338 7987 Z= 0.329 Chirality : 0.043 0.180 961 Planarity : 0.005 0.065 972 Dihedral : 4.758 42.369 863 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.57 % Allowed : 30.66 % 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: 1.40 (0.31), residues: 751 helix: 1.50 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -1.49 (0.47), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 336 HIS 0.002 0.000 HIS B 167 PHE 0.017 0.001 PHE B 356 TYR 0.016 0.001 TYR A 476 ARG 0.001 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 450) hydrogen bonds : angle 4.13512 ( 1323) covalent geometry : bond 0.00327 ( 5863) covalent geometry : angle 0.69855 ( 7987) *********************** 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 195 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7381 (tt0) cc_final: 0.7114 (tt0) REVERT: A 39 THR cc_start: 0.8280 (t) cc_final: 0.8015 (t) REVERT: A 249 VAL cc_start: 0.7740 (m) cc_final: 0.7055 (p) REVERT: A 250 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.6808 (mpp) REVERT: A 253 PHE cc_start: 0.7076 (m-80) cc_final: 0.6833 (m-80) REVERT: A 374 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8230 (mt) REVERT: A 474 LEU cc_start: 0.7824 (mt) cc_final: 0.7493 (mp) REVERT: A 476 TYR cc_start: 0.8128 (t80) cc_final: 0.7637 (t80) REVERT: B 127 GLN cc_start: 0.5437 (OUTLIER) cc_final: 0.4986 (tm-30) REVERT: B 170 MET cc_start: 0.6855 (tpp) cc_final: 0.6556 (tpp) REVERT: B 452 VAL cc_start: 0.7425 (m) cc_final: 0.7159 (p) REVERT: B 461 MET cc_start: 0.6857 (mmm) cc_final: 0.6498 (mmt) outliers start: 34 outliers final: 22 residues processed: 179 average time/residue: 0.1319 time to fit residues: 33.2910 Evaluate side-chains 183 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL 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 205 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 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 405 MET 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 44 ILE Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 132 LEU 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 381 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 0.0010 chunk 66 optimal weight: 0.0020 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 ASN ** 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 = 0.3869 r_free = 0.3869 target = 0.139714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.126619 restraints weight = 9017.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.130575 restraints weight = 4448.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.133076 restraints weight = 2532.070| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5863 Z= 0.161 Angle : 0.720 10.195 7987 Z= 0.339 Chirality : 0.044 0.238 961 Planarity : 0.005 0.064 972 Dihedral : 4.732 42.829 863 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.75 % Allowed : 30.98 % Favored : 64.26 % 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: 1.32 (0.31), residues: 751 helix: 1.42 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -1.38 (0.47), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 366 HIS 0.002 0.001 HIS B 167 PHE 0.016 0.001 PHE B 356 TYR 0.019 0.001 TYR A 476 ARG 0.002 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 450) hydrogen bonds : angle 4.17504 ( 1323) covalent geometry : bond 0.00375 ( 5863) covalent geometry : angle 0.72046 ( 7987) ********************** 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 to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7380 (tt0) cc_final: 0.7123 (tt0) REVERT: A 249 VAL cc_start: 0.7756 (m) cc_final: 0.7062 (p) REVERT: A 250 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.6831 (mpp) REVERT: A 253 PHE cc_start: 0.7094 (m-80) cc_final: 0.6842 (m-80) REVERT: A 474 LEU cc_start: 0.7843 (mt) cc_final: 0.7497 (mp) REVERT: A 476 TYR cc_start: 0.8140 (t80) cc_final: 0.7668 (t80) REVERT: B 127 GLN cc_start: 0.5467 (OUTLIER) cc_final: 0.4949 (tm-30) REVERT: B 170 MET cc_start: 0.6924 (tpp) cc_final: 0.6565 (tpp) REVERT: B 302 ILE cc_start: 0.7758 (mm) cc_final: 0.7534 (mt) REVERT: B 452 VAL cc_start: 0.7431 (m) cc_final: 0.7172 (p) REVERT: B 461 MET cc_start: 0.6872 (mmm) cc_final: 0.6562 (mmt) outliers start: 29 outliers final: 24 residues processed: 179 average time/residue: 0.1804 time to fit residues: 45.1924 Evaluate side-chains 189 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL 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 205 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 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 405 MET 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 44 ILE Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 297 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 68 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 66 optimal weight: 0.0010 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 57 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.139516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.126603 restraints weight = 8972.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.130516 restraints weight = 4442.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.133013 restraints weight = 2533.541| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2367 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= 0.165 Angle : 0.716 10.790 7987 Z= 0.340 Chirality : 0.044 0.252 961 Planarity : 0.005 0.061 972 Dihedral : 4.766 42.706 863 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.59 % Allowed : 31.15 % Favored : 64.26 % 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: 1.33 (0.31), residues: 751 helix: 1.42 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -1.36 (0.48), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.002 0.001 HIS B 167 PHE 0.017 0.001 PHE B 356 TYR 0.019 0.001 TYR A 476 ARG 0.002 0.000 ARG A 421 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 450) hydrogen bonds : angle 4.18306 ( 1323) covalent geometry : bond 0.00382 ( 5863) covalent geometry : angle 0.71585 ( 7987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2159.56 seconds wall clock time: 39 minutes 49.08 seconds (2389.08 seconds total)