Starting phenix.real_space_refine on Thu Mar 13 09:19:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axc_43932/03_2025/9axc_43932.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axc_43932/03_2025/9axc_43932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9axc_43932/03_2025/9axc_43932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axc_43932/03_2025/9axc_43932.map" model { file = "/net/cci-nas-00/data/ceres_data/9axc_43932/03_2025/9axc_43932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axc_43932/03_2025/9axc_43932.cif" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 5566 2.51 5 N 1479 2.21 5 O 1568 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8677 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2120 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain breaks: 2 Chain: "B" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2186 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 12, 'TRANS': 265} Chain breaks: 2 Chain: "C" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2137 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 11, 'TRANS': 252} Chain breaks: 2 Chain: "D" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2166 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 2 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'A1AHE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'A1AHE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.85, per 1000 atoms: 0.56 Number of scatterers: 8677 At special positions: 0 Unit cell: (85.0935, 164.756, 65.178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 F 4 9.00 O 1568 8.00 N 1479 7.00 C 5566 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: 1.88 Conformation dependent library (CDL) restraints added in 1.2 seconds 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 50.6% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.747A pdb=" N GLU A 348 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 399 removed outlier: 3.911A pdb=" N LYS A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 Processing helix chain 'A' and resid 441 through 462 removed outlier: 3.578A pdb=" N LEU A 445 " --> pdb=" O GLN A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 513 through 519 Processing helix chain 'A' and resid 526 through 544 removed outlier: 3.719A pdb=" N ASP A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 569 through 573 removed outlier: 4.331A pdb=" N LYS A 572 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 589 removed outlier: 3.553A pdb=" N LYS A 582 " --> pdb=" O PRO A 578 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 589 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 596 removed outlier: 3.759A pdb=" N GLU A 595 " --> pdb=" O VAL A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 612 removed outlier: 3.795A pdb=" N SER A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 removed outlier: 3.757A pdb=" N LYS B 57 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 117 through 120 Processing helix chain 'B' and resid 150 through 159 removed outlier: 3.784A pdb=" N VAL B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 184 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 241 through 259 removed outlier: 4.094A pdb=" N ASP B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 331 through 342 removed outlier: 3.821A pdb=" N GLN B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 358 through 367 Processing helix chain 'B' and resid 370 through 380 removed outlier: 3.585A pdb=" N TRP B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 398 removed outlier: 3.803A pdb=" N ALA C 389 " --> pdb=" O GLU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 435 Processing helix chain 'C' and resid 441 through 462 Processing helix chain 'C' and resid 478 through 480 No H-bonds generated for 'chain 'C' and resid 478 through 480' Processing helix chain 'C' and resid 486 through 490 removed outlier: 4.658A pdb=" N LEU C 489 " --> pdb=" O ASP C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 519 Processing helix chain 'C' and resid 526 through 544 removed outlier: 3.828A pdb=" N ASP C 530 " --> pdb=" O SER C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 563 Processing helix chain 'C' and resid 569 through 573 removed outlier: 3.698A pdb=" N LYS C 572 " --> pdb=" O ASP C 569 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 573 " --> pdb=" O LEU C 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 569 through 573' Processing helix chain 'C' and resid 578 through 588 Processing helix chain 'C' and resid 598 through 613 Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 104 through 114 Processing helix chain 'D' and resid 115 through 121 removed outlier: 3.699A pdb=" N LEU D 118 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 159 Processing helix chain 'D' and resid 162 through 185 Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 231 through 236 removed outlier: 3.960A pdb=" N GLN D 236 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 259 removed outlier: 4.176A pdb=" N ASP D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 320 removed outlier: 3.955A pdb=" N GLU D 320 " --> pdb=" O TYR D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 342 removed outlier: 3.597A pdb=" N GLN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 356 Processing helix chain 'D' and resid 358 through 367 removed outlier: 3.518A pdb=" N LYS D 362 " --> pdb=" O HIS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 350 through 354 removed outlier: 5.971A pdb=" N LEU A 351 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS A 367 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 417 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 418 " --> pdb=" O MET A 412 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN A 422 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE A 408 " --> pdb=" O GLN A 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 426 through 428 removed outlier: 4.211A pdb=" N SER A 427 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 87 removed outlier: 3.574A pdb=" N HIS B 87 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B 92 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY B 131 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLU B 144 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE B 129 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 196 through 198 Processing sheet with id=AA5, first strand: chain 'C' and resid 365 through 367 removed outlier: 6.498A pdb=" N GLN C 422 " --> pdb=" O PHE C 408 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE C 408 " --> pdb=" O GLN C 422 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 474 through 477 Processing sheet with id=AA7, first strand: chain 'D' and resid 72 through 73 removed outlier: 3.673A pdb=" N ILE D 99 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 139 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY D 131 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU D 144 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE D 129 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 196 through 198 395 hydrogen bonds defined for protein. 1122 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: 2.42 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2427 1.34 - 1.46: 1609 1.46 - 1.58: 4721 1.58 - 1.70: 3 1.70 - 1.82: 101 Bond restraints: 8861 Sorted by residual: bond pdb=" N PHE A 443 " pdb=" CA PHE A 443 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.17e-02 7.31e+03 1.09e+01 bond pdb=" N VAL D 254 " pdb=" CA VAL D 254 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 8.19e+00 bond pdb=" N VAL B 117 " pdb=" CA VAL B 117 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.24e-02 6.50e+03 7.25e+00 bond pdb=" C07 A1AHE D 401 " pdb=" N06 A1AHE D 401 " ideal model delta sigma weight residual 1.390 1.442 -0.052 2.00e-02 2.50e+03 6.68e+00 bond pdb=" N GLN A 441 " pdb=" CA GLN A 441 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.16e-02 7.43e+03 6.65e+00 ... (remaining 8856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 11477 2.33 - 4.67: 381 4.67 - 7.00: 68 7.00 - 9.33: 24 9.33 - 11.66: 2 Bond angle restraints: 11952 Sorted by residual: angle pdb=" CB MET C 456 " pdb=" CG MET C 456 " pdb=" SD MET C 456 " ideal model delta sigma weight residual 112.70 101.04 11.66 3.00e+00 1.11e-01 1.51e+01 angle pdb=" CB ARG C 583 " pdb=" CG ARG C 583 " pdb=" CD ARG C 583 " ideal model delta sigma weight residual 111.30 120.03 -8.73 2.30e+00 1.89e-01 1.44e+01 angle pdb=" C PRO C 505 " pdb=" N THR C 506 " pdb=" CA THR C 506 " ideal model delta sigma weight residual 121.54 128.56 -7.02 1.91e+00 2.74e-01 1.35e+01 angle pdb=" CA PHE A 443 " pdb=" CB PHE A 443 " pdb=" CG PHE A 443 " ideal model delta sigma weight residual 113.80 117.39 -3.59 1.00e+00 1.00e+00 1.29e+01 angle pdb=" C TRP C 342 " pdb=" N GLU C 343 " pdb=" CA GLU C 343 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 ... (remaining 11947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4898 17.96 - 35.91: 390 35.91 - 53.87: 68 53.87 - 71.83: 21 71.83 - 89.78: 6 Dihedral angle restraints: 5383 sinusoidal: 2260 harmonic: 3123 Sorted by residual: dihedral pdb=" CA MET D 146 " pdb=" C MET D 146 " pdb=" N ASP D 147 " pdb=" CA ASP D 147 " ideal model delta harmonic sigma weight residual -180.00 -145.67 -34.33 0 5.00e+00 4.00e-02 4.71e+01 dihedral pdb=" CA GLN B 354 " pdb=" C GLN B 354 " pdb=" N LEU B 355 " pdb=" CA LEU B 355 " ideal model delta harmonic sigma weight residual 180.00 153.58 26.42 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA GLU D 114 " pdb=" C GLU D 114 " pdb=" N LEU D 115 " pdb=" CA LEU D 115 " ideal model delta harmonic sigma weight residual 180.00 154.00 26.00 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 5380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 767 0.040 - 0.079: 335 0.079 - 0.119: 146 0.119 - 0.159: 49 0.159 - 0.198: 17 Chirality restraints: 1314 Sorted by residual: chirality pdb=" CG LEU D 314 " pdb=" CB LEU D 314 " pdb=" CD1 LEU D 314 " pdb=" CD2 LEU D 314 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CA VAL D 254 " pdb=" N VAL D 254 " pdb=" C VAL D 254 " pdb=" CB VAL D 254 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.93e-01 chirality pdb=" CA PHE C 599 " pdb=" N PHE C 599 " pdb=" C PHE C 599 " pdb=" CB PHE C 599 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 1311 not shown) Planarity restraints: 1511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 554 " 0.501 9.50e-02 1.11e+02 2.26e-01 4.13e+01 pdb=" NE ARG C 554 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG C 554 " 0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG C 554 " -0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG C 554 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 381 " 0.046 5.00e-02 4.00e+02 7.08e-02 8.01e+00 pdb=" N PRO A 382 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 247 " -0.018 2.00e-02 2.50e+03 1.50e-02 5.66e+00 pdb=" CG TRP B 247 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 247 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 247 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 247 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 247 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 247 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 247 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 247 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 247 " -0.002 2.00e-02 2.50e+03 ... (remaining 1508 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1572 2.77 - 3.31: 8343 3.31 - 3.84: 14200 3.84 - 4.37: 16142 4.37 - 4.90: 27342 Nonbonded interactions: 67599 Sorted by model distance: nonbonded pdb=" OE1 GLN A 436 " pdb=" OG1 THR A 438 " model vdw 2.243 3.040 nonbonded pdb=" OG SER B 150 " pdb=" OE1 GLN B 153 " model vdw 2.268 3.040 nonbonded pdb=" O LYS C 399 " pdb=" NZ LYS C 462 " model vdw 2.293 3.120 nonbonded pdb=" O ILE B 343 " pdb=" NH1 ARG B 349 " model vdw 2.316 3.120 nonbonded pdb=" NE2 GLN B 243 " pdb=" OD1 ASP B 351 " model vdw 2.328 3.120 ... (remaining 67594 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 342 through 354 or resid 362 through 376 or resid 382 thro \ ugh 614)) selection = (chain 'C' and (resid 342 through 354 or resid 362 through 494 or resid 500 thro \ ugh 614)) } ncs_group { reference = (chain 'B' and (resid 59 through 72 or resid 81 through 380 or resid 401)) selection = (chain 'D' and (resid 59 through 72 or resid 81 through 380 or resid 401)) } 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: 6.440 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.380 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8861 Z= 0.313 Angle : 1.004 11.665 11952 Z= 0.510 Chirality : 0.057 0.198 1314 Planarity : 0.009 0.226 1511 Dihedral : 13.776 89.785 3363 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.17 % Favored : 95.64 % Rotamer: Outliers : 0.21 % Allowed : 1.47 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.06 (0.24), residues: 1055 helix: -0.55 (0.23), residues: 445 sheet: 0.47 (0.64), residues: 70 loop : -0.92 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 247 HIS 0.013 0.001 HIS A 477 PHE 0.040 0.003 PHE D 337 TYR 0.022 0.002 TYR B 229 ARG 0.056 0.002 ARG C 554 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 236 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.8465 (m-10) cc_final: 0.8156 (m-80) REVERT: A 391 ARG cc_start: 0.8696 (mtt180) cc_final: 0.8452 (mmm-85) REVERT: A 409 MET cc_start: 0.9261 (mtt) cc_final: 0.8769 (mpp) REVERT: A 447 ASP cc_start: 0.8951 (m-30) cc_final: 0.8628 (m-30) REVERT: A 486 ASP cc_start: 0.8372 (t0) cc_final: 0.8115 (t70) REVERT: A 552 ASN cc_start: 0.7581 (p0) cc_final: 0.7178 (p0) REVERT: B 197 LEU cc_start: 0.8484 (mm) cc_final: 0.8282 (mm) REVERT: C 393 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7380 (mt-10) REVERT: C 456 MET cc_start: 0.9305 (mmt) cc_final: 0.9081 (mmm) REVERT: C 537 VAL cc_start: 0.9143 (t) cc_final: 0.8940 (t) REVERT: C 598 LEU cc_start: 0.8548 (mt) cc_final: 0.8253 (mt) REVERT: D 94 MET cc_start: 0.8599 (mpp) cc_final: 0.8154 (mpp) REVERT: D 199 ASN cc_start: 0.8830 (t0) cc_final: 0.8482 (t0) REVERT: D 209 PHE cc_start: 0.8645 (p90) cc_final: 0.8327 (p90) REVERT: D 240 TYR cc_start: 0.7501 (p90) cc_final: 0.6932 (p90) REVERT: D 317 ILE cc_start: 0.9375 (mm) cc_final: 0.9163 (mm) REVERT: D 343 ILE cc_start: 0.7782 (mt) cc_final: 0.7482 (mt) outliers start: 2 outliers final: 1 residues processed: 236 average time/residue: 0.2425 time to fit residues: 79.6783 Evaluate side-chains 183 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.0670 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.103174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.082124 restraints weight = 25854.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.084591 restraints weight = 15034.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.086266 restraints weight = 10369.017| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8861 Z= 0.191 Angle : 0.590 5.800 11952 Z= 0.311 Chirality : 0.045 0.160 1314 Planarity : 0.005 0.043 1511 Dihedral : 4.993 29.448 1210 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.13 % Favored : 96.68 % Rotamer: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.64 % 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: -0.15 (0.25), residues: 1055 helix: 0.47 (0.24), residues: 469 sheet: 0.46 (0.58), residues: 89 loop : -0.69 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 247 HIS 0.010 0.001 HIS A 477 PHE 0.014 0.001 PHE D 337 TYR 0.013 0.001 TYR A 532 ARG 0.004 0.001 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.7713 (mmm) cc_final: 0.7306 (mmm) REVERT: A 436 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 473 ASN cc_start: 0.8616 (m110) cc_final: 0.8242 (m110) REVERT: A 486 ASP cc_start: 0.8575 (t0) cc_final: 0.8137 (t0) REVERT: A 523 ASN cc_start: 0.8067 (t0) cc_final: 0.7600 (p0) REVERT: A 532 TYR cc_start: 0.7925 (t80) cc_final: 0.7636 (t80) REVERT: A 552 ASN cc_start: 0.7919 (p0) cc_final: 0.7602 (p0) REVERT: B 182 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8292 (mm-30) REVERT: B 253 LEU cc_start: 0.9246 (mm) cc_final: 0.8968 (mm) REVERT: C 393 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7365 (mt-10) REVERT: C 401 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7856 (mtp85) REVERT: C 417 LEU cc_start: 0.9308 (mt) cc_final: 0.9103 (mt) REVERT: C 442 MET cc_start: 0.8671 (mmp) cc_final: 0.8411 (mtt) REVERT: C 444 GLN cc_start: 0.8859 (mt0) cc_final: 0.8535 (mt0) REVERT: C 469 MET cc_start: 0.8442 (mmp) cc_final: 0.8158 (tpp) REVERT: C 481 THR cc_start: 0.8867 (m) cc_final: 0.8614 (m) REVERT: D 94 MET cc_start: 0.8045 (mpp) cc_final: 0.7564 (mpp) REVERT: D 114 GLU cc_start: 0.8747 (mp0) cc_final: 0.8542 (mp0) REVERT: D 199 ASN cc_start: 0.8841 (t0) cc_final: 0.8552 (t0) REVERT: D 209 PHE cc_start: 0.8956 (p90) cc_final: 0.8667 (p90) REVERT: D 240 TYR cc_start: 0.7375 (p90) cc_final: 0.6845 (p90) REVERT: D 317 ILE cc_start: 0.9397 (mm) cc_final: 0.9186 (mm) REVERT: D 343 ILE cc_start: 0.7825 (mt) cc_final: 0.7372 (mt) outliers start: 1 outliers final: 0 residues processed: 240 average time/residue: 0.1873 time to fit residues: 63.0001 Evaluate side-chains 185 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 44 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 46 optimal weight: 0.0170 chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 overall best weight: 2.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.097093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.076710 restraints weight = 26513.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.079148 restraints weight = 15216.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.080790 restraints weight = 10413.036| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8861 Z= 0.301 Angle : 0.649 6.383 11952 Z= 0.342 Chirality : 0.047 0.155 1314 Planarity : 0.005 0.055 1511 Dihedral : 5.312 32.033 1210 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.98 % Favored : 95.83 % Rotamer: Outliers : 0.10 % Allowed : 5.25 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.16 (0.25), residues: 1055 helix: 0.62 (0.24), residues: 468 sheet: -0.05 (0.66), residues: 61 loop : -0.73 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 247 HIS 0.008 0.002 HIS A 477 PHE 0.027 0.002 PHE A 387 TYR 0.019 0.002 TYR D 134 ARG 0.005 0.001 ARG D 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.7788 (mmm) cc_final: 0.7001 (mmm) REVERT: A 436 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7809 (tm-30) REVERT: A 473 ASN cc_start: 0.8836 (m110) cc_final: 0.8387 (m-40) REVERT: A 486 ASP cc_start: 0.8651 (t0) cc_final: 0.8270 (t70) REVERT: A 523 ASN cc_start: 0.8155 (t0) cc_final: 0.7949 (p0) REVERT: A 552 ASN cc_start: 0.7917 (p0) cc_final: 0.7696 (p0) REVERT: A 553 ASN cc_start: 0.9131 (t0) cc_final: 0.8783 (t0) REVERT: B 99 ILE cc_start: 0.8895 (mm) cc_final: 0.8602 (mm) REVERT: B 143 MET cc_start: 0.7939 (ptp) cc_final: 0.7734 (ptp) REVERT: B 182 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8470 (mm-30) REVERT: B 190 ASP cc_start: 0.8438 (t0) cc_final: 0.7750 (t0) REVERT: B 197 LEU cc_start: 0.8779 (mm) cc_final: 0.8567 (mm) REVERT: B 230 MET cc_start: 0.8379 (tpp) cc_final: 0.8104 (tpp) REVERT: B 246 ILE cc_start: 0.9470 (mt) cc_final: 0.8935 (mt) REVERT: B 249 MET cc_start: 0.9121 (tmm) cc_final: 0.8561 (tmm) REVERT: B 253 LEU cc_start: 0.9270 (mm) cc_final: 0.8861 (mm) REVERT: B 324 LYS cc_start: 0.6168 (ptpp) cc_final: 0.5781 (mmtt) REVERT: B 341 CYS cc_start: 0.8029 (m) cc_final: 0.7709 (t) REVERT: C 385 GLU cc_start: 0.8460 (pm20) cc_final: 0.7692 (pm20) REVERT: C 393 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7508 (mt-10) REVERT: C 444 GLN cc_start: 0.8821 (mt0) cc_final: 0.8440 (mt0) REVERT: C 456 MET cc_start: 0.9344 (mmm) cc_final: 0.9098 (mmt) REVERT: C 458 TYR cc_start: 0.8970 (t80) cc_final: 0.8539 (t80) REVERT: C 521 ASP cc_start: 0.7264 (t70) cc_final: 0.6852 (t70) REVERT: C 553 ASN cc_start: 0.8687 (t0) cc_final: 0.8274 (t0) REVERT: C 583 ARG cc_start: 0.8466 (tpm170) cc_final: 0.8152 (tpm170) REVERT: D 94 MET cc_start: 0.8025 (mpp) cc_final: 0.7491 (mpp) REVERT: D 199 ASN cc_start: 0.8770 (t0) cc_final: 0.8130 (t0) REVERT: D 209 PHE cc_start: 0.9082 (p90) cc_final: 0.8627 (p90) REVERT: D 317 ILE cc_start: 0.9318 (mm) cc_final: 0.9053 (mm) REVERT: D 343 ILE cc_start: 0.8132 (mt) cc_final: 0.7730 (mt) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.1902 time to fit residues: 62.1198 Evaluate side-chains 177 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.097724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.077269 restraints weight = 26480.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.079739 restraints weight = 15007.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.081422 restraints weight = 10224.386| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8861 Z= 0.249 Angle : 0.604 6.160 11952 Z= 0.318 Chirality : 0.046 0.237 1314 Planarity : 0.005 0.090 1511 Dihedral : 5.112 31.602 1210 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.79 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1055 helix: 0.91 (0.24), residues: 467 sheet: -0.09 (0.67), residues: 61 loop : -0.62 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 247 HIS 0.006 0.001 HIS A 477 PHE 0.025 0.002 PHE B 133 TYR 0.013 0.002 TYR D 134 ARG 0.004 0.001 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8047 (mmm) cc_final: 0.7166 (mmm) REVERT: A 417 LEU cc_start: 0.9048 (mt) cc_final: 0.8546 (pt) REVERT: A 436 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7844 (tm-30) REVERT: A 443 PHE cc_start: 0.8549 (p90) cc_final: 0.8153 (p90) REVERT: A 456 MET cc_start: 0.9257 (mmm) cc_final: 0.9051 (mmm) REVERT: A 473 ASN cc_start: 0.8767 (m110) cc_final: 0.8280 (m-40) REVERT: A 486 ASP cc_start: 0.8511 (t0) cc_final: 0.8116 (t70) REVERT: A 504 GLN cc_start: 0.8177 (mm110) cc_final: 0.7184 (pm20) REVERT: A 552 ASN cc_start: 0.7942 (p0) cc_final: 0.7711 (p0) REVERT: A 553 ASN cc_start: 0.9130 (t0) cc_final: 0.8755 (t0) REVERT: B 182 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8575 (mm-30) REVERT: B 190 ASP cc_start: 0.8560 (t0) cc_final: 0.7720 (t0) REVERT: B 197 LEU cc_start: 0.8837 (mm) cc_final: 0.8636 (mm) REVERT: B 230 MET cc_start: 0.8444 (tpp) cc_final: 0.7974 (tpp) REVERT: B 249 MET cc_start: 0.9298 (tmm) cc_final: 0.8912 (tmm) REVERT: B 253 LEU cc_start: 0.9285 (mm) cc_final: 0.8786 (mm) REVERT: B 314 LEU cc_start: 0.9141 (mt) cc_final: 0.8916 (mt) REVERT: B 324 LYS cc_start: 0.6683 (ptpp) cc_final: 0.6080 (mmtt) REVERT: C 412 MET cc_start: 0.5867 (ttt) cc_final: 0.5566 (tmm) REVERT: C 442 MET cc_start: 0.8800 (mmp) cc_final: 0.8168 (ttt) REVERT: C 444 GLN cc_start: 0.8908 (mt0) cc_final: 0.8458 (mt0) REVERT: C 458 TYR cc_start: 0.8981 (t80) cc_final: 0.8455 (t80) REVERT: C 521 ASP cc_start: 0.7034 (t70) cc_final: 0.6648 (t70) REVERT: D 94 MET cc_start: 0.8064 (mpp) cc_final: 0.7514 (mpp) REVERT: D 199 ASN cc_start: 0.8811 (t0) cc_final: 0.8454 (t0) REVERT: D 209 PHE cc_start: 0.9149 (p90) cc_final: 0.8763 (p90) REVERT: D 317 ILE cc_start: 0.9278 (mm) cc_final: 0.9050 (mt) REVERT: D 343 ILE cc_start: 0.8312 (mt) cc_final: 0.7764 (mt) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1803 time to fit residues: 60.4298 Evaluate side-chains 176 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 20 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 95 optimal weight: 0.0870 chunk 40 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.079393 restraints weight = 25996.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.082006 restraints weight = 14609.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083740 restraints weight = 9848.399| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8861 Z= 0.160 Angle : 0.554 5.736 11952 Z= 0.291 Chirality : 0.045 0.142 1314 Planarity : 0.004 0.094 1511 Dihedral : 4.734 30.608 1210 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.51 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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: 0.37 (0.26), residues: 1055 helix: 1.13 (0.24), residues: 467 sheet: 0.31 (0.66), residues: 65 loop : -0.54 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 247 HIS 0.006 0.001 HIS D 100 PHE 0.022 0.001 PHE A 390 TYR 0.021 0.001 TYR D 134 ARG 0.006 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8147 (mmm) cc_final: 0.7602 (mmt) REVERT: A 436 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7769 (tm-30) REVERT: A 456 MET cc_start: 0.9319 (mmm) cc_final: 0.9040 (mmm) REVERT: A 486 ASP cc_start: 0.8431 (t0) cc_final: 0.7947 (t0) REVERT: A 504 GLN cc_start: 0.8128 (mm110) cc_final: 0.7143 (pm20) REVERT: A 552 ASN cc_start: 0.7906 (p0) cc_final: 0.7658 (p0) REVERT: A 553 ASN cc_start: 0.9146 (t0) cc_final: 0.8797 (t0) REVERT: A 560 MET cc_start: 0.8528 (mmm) cc_final: 0.8326 (mmm) REVERT: B 182 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8687 (mm-30) REVERT: B 190 ASP cc_start: 0.8498 (t0) cc_final: 0.7662 (t0) REVERT: B 224 VAL cc_start: 0.8227 (m) cc_final: 0.7954 (p) REVERT: B 249 MET cc_start: 0.9309 (tmm) cc_final: 0.8857 (tmm) REVERT: B 253 LEU cc_start: 0.9252 (mm) cc_final: 0.8784 (mm) REVERT: B 314 LEU cc_start: 0.9051 (mt) cc_final: 0.8834 (mt) REVERT: B 324 LYS cc_start: 0.6756 (ptpp) cc_final: 0.6097 (mmtt) REVERT: C 401 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7754 (mtp85) REVERT: C 412 MET cc_start: 0.6302 (ttt) cc_final: 0.5160 (tmm) REVERT: C 444 GLN cc_start: 0.8844 (mt0) cc_final: 0.8439 (mt0) REVERT: C 458 TYR cc_start: 0.8973 (t80) cc_final: 0.8471 (t80) REVERT: C 469 MET cc_start: 0.9479 (mmp) cc_final: 0.9184 (tpp) REVERT: C 493 LYS cc_start: 0.9232 (tppt) cc_final: 0.8737 (tptt) REVERT: C 521 ASP cc_start: 0.7039 (t70) cc_final: 0.6712 (t70) REVERT: C 534 TYR cc_start: 0.9146 (t80) cc_final: 0.8819 (t80) REVERT: C 553 ASN cc_start: 0.8555 (t0) cc_final: 0.8245 (t0) REVERT: D 94 MET cc_start: 0.8252 (mpp) cc_final: 0.7859 (mpp) REVERT: D 134 TYR cc_start: 0.8517 (t80) cc_final: 0.8231 (t80) REVERT: D 209 PHE cc_start: 0.9092 (p90) cc_final: 0.8768 (p90) REVERT: D 308 MET cc_start: 0.5026 (ptp) cc_final: 0.4704 (ptm) REVERT: D 310 ILE cc_start: 0.8102 (tp) cc_final: 0.7571 (tt) REVERT: D 317 ILE cc_start: 0.9344 (mm) cc_final: 0.9091 (mm) REVERT: D 343 ILE cc_start: 0.8126 (mt) cc_final: 0.7568 (mt) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2355 time to fit residues: 86.5601 Evaluate side-chains 192 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.097936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.077610 restraints weight = 26455.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.080109 restraints weight = 14917.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.081779 restraints weight = 10109.094| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8861 Z= 0.216 Angle : 0.588 8.035 11952 Z= 0.308 Chirality : 0.045 0.136 1314 Planarity : 0.004 0.066 1511 Dihedral : 4.855 31.961 1210 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.89 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: 0.29 (0.26), residues: 1055 helix: 1.04 (0.24), residues: 473 sheet: 0.19 (0.68), residues: 55 loop : -0.55 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 247 HIS 0.009 0.001 HIS C 466 PHE 0.021 0.002 PHE D 337 TYR 0.019 0.002 TYR C 534 ARG 0.005 0.001 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8442 (mmm) cc_final: 0.7247 (mmm) REVERT: A 436 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7746 (tm-30) REVERT: A 447 ASP cc_start: 0.8996 (m-30) cc_final: 0.8795 (m-30) REVERT: A 456 MET cc_start: 0.9257 (mmm) cc_final: 0.8966 (mmm) REVERT: A 486 ASP cc_start: 0.8399 (t0) cc_final: 0.8192 (t70) REVERT: A 504 GLN cc_start: 0.8067 (mm110) cc_final: 0.6978 (pm20) REVERT: A 552 ASN cc_start: 0.7879 (p0) cc_final: 0.7673 (p0) REVERT: A 553 ASN cc_start: 0.9126 (t0) cc_final: 0.8771 (t0) REVERT: B 99 ILE cc_start: 0.8865 (mm) cc_final: 0.8595 (mm) REVERT: B 182 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8671 (mm-30) REVERT: B 190 ASP cc_start: 0.8490 (t0) cc_final: 0.7635 (t0) REVERT: B 197 LEU cc_start: 0.8634 (mm) cc_final: 0.8432 (mm) REVERT: B 224 VAL cc_start: 0.8158 (m) cc_final: 0.7898 (p) REVERT: B 249 MET cc_start: 0.9353 (tmm) cc_final: 0.8901 (tmm) REVERT: B 253 LEU cc_start: 0.9252 (mm) cc_final: 0.8929 (mm) REVERT: B 324 LYS cc_start: 0.6489 (ptpp) cc_final: 0.5873 (mmtt) REVERT: C 412 MET cc_start: 0.5746 (ttt) cc_final: 0.5172 (tmm) REVERT: C 442 MET cc_start: 0.8791 (mmp) cc_final: 0.7976 (mtp) REVERT: C 444 GLN cc_start: 0.8829 (mt0) cc_final: 0.8437 (mt0) REVERT: C 458 TYR cc_start: 0.9011 (t80) cc_final: 0.8408 (t80) REVERT: C 469 MET cc_start: 0.9486 (mmp) cc_final: 0.9063 (tpp) REVERT: C 521 ASP cc_start: 0.7199 (t70) cc_final: 0.6872 (t70) REVERT: C 522 ASN cc_start: 0.7584 (t0) cc_final: 0.7170 (t0) REVERT: C 553 ASN cc_start: 0.8685 (t0) cc_final: 0.8322 (t0) REVERT: C 583 ARG cc_start: 0.8482 (tpp-160) cc_final: 0.8038 (tpm170) REVERT: D 94 MET cc_start: 0.8250 (mpp) cc_final: 0.7944 (mpp) REVERT: D 134 TYR cc_start: 0.8569 (t80) cc_final: 0.8265 (t80) REVERT: D 209 PHE cc_start: 0.9125 (p90) cc_final: 0.8766 (p90) REVERT: D 249 MET cc_start: 0.8719 (ppp) cc_final: 0.8286 (ppp) REVERT: D 308 MET cc_start: 0.4340 (ptp) cc_final: 0.4000 (ptm) REVERT: D 317 ILE cc_start: 0.9515 (mm) cc_final: 0.9249 (mt) REVERT: D 343 ILE cc_start: 0.8200 (mt) cc_final: 0.7787 (mt) REVERT: D 378 THR cc_start: 0.7877 (m) cc_final: 0.6653 (m) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2156 time to fit residues: 74.5937 Evaluate side-chains 188 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 65 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.098969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.078797 restraints weight = 25958.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.081316 restraints weight = 14413.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.083077 restraints weight = 9713.317| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8861 Z= 0.167 Angle : 0.573 7.198 11952 Z= 0.300 Chirality : 0.045 0.170 1314 Planarity : 0.004 0.052 1511 Dihedral : 4.739 31.134 1210 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.41 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: 0.40 (0.26), residues: 1055 helix: 1.12 (0.24), residues: 473 sheet: 0.34 (0.67), residues: 64 loop : -0.51 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 247 HIS 0.019 0.001 HIS C 477 PHE 0.016 0.001 PHE A 443 TYR 0.022 0.001 TYR C 534 ARG 0.003 0.000 ARG A 554 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.8143 (m-80) cc_final: 0.7759 (m-80) REVERT: A 412 MET cc_start: 0.8528 (mmm) cc_final: 0.8016 (mmp) REVERT: A 417 LEU cc_start: 0.9028 (mt) cc_final: 0.8441 (pt) REVERT: A 436 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7869 (tm-30) REVERT: A 441 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8534 (tm-30) REVERT: A 486 ASP cc_start: 0.8305 (t0) cc_final: 0.7731 (t0) REVERT: A 504 GLN cc_start: 0.8054 (mm110) cc_final: 0.6966 (pm20) REVERT: A 532 TYR cc_start: 0.8540 (t80) cc_final: 0.8063 (t80) REVERT: A 553 ASN cc_start: 0.9048 (t0) cc_final: 0.8732 (t0) REVERT: B 182 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8675 (mm-30) REVERT: B 190 ASP cc_start: 0.8509 (t0) cc_final: 0.7547 (t0) REVERT: B 224 VAL cc_start: 0.8220 (m) cc_final: 0.7971 (p) REVERT: B 230 MET cc_start: 0.8287 (tpp) cc_final: 0.7978 (tpp) REVERT: B 249 MET cc_start: 0.9315 (tmm) cc_final: 0.8854 (tmm) REVERT: B 253 LEU cc_start: 0.9213 (mm) cc_final: 0.8672 (mm) REVERT: B 324 LYS cc_start: 0.6534 (ptpp) cc_final: 0.5872 (mmtt) REVERT: C 412 MET cc_start: 0.6208 (ttt) cc_final: 0.5404 (tmm) REVERT: C 442 MET cc_start: 0.8761 (mmp) cc_final: 0.7986 (mtp) REVERT: C 444 GLN cc_start: 0.8788 (mt0) cc_final: 0.8419 (mt0) REVERT: C 469 MET cc_start: 0.9405 (mmp) cc_final: 0.8898 (tpp) REVERT: C 521 ASP cc_start: 0.7590 (t70) cc_final: 0.7218 (t70) REVERT: C 583 ARG cc_start: 0.8465 (tpp-160) cc_final: 0.8261 (tpm170) REVERT: D 134 TYR cc_start: 0.8626 (t80) cc_final: 0.8317 (t80) REVERT: D 199 ASN cc_start: 0.8861 (t0) cc_final: 0.8658 (t0) REVERT: D 209 PHE cc_start: 0.9054 (p90) cc_final: 0.8758 (p90) REVERT: D 249 MET cc_start: 0.8744 (ppp) cc_final: 0.8438 (ppp) REVERT: D 308 MET cc_start: 0.4364 (ptp) cc_final: 0.4026 (ptm) REVERT: D 317 ILE cc_start: 0.9509 (mm) cc_final: 0.9256 (mt) REVERT: D 343 ILE cc_start: 0.8164 (mt) cc_final: 0.7709 (mt) REVERT: D 378 THR cc_start: 0.7909 (m) cc_final: 0.6525 (m) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.1733 time to fit residues: 59.3831 Evaluate side-chains 186 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 33 optimal weight: 0.0870 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.095361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.074989 restraints weight = 27095.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.077425 restraints weight = 15452.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.079084 restraints weight = 10513.913| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8861 Z= 0.303 Angle : 0.663 8.603 11952 Z= 0.347 Chirality : 0.048 0.189 1314 Planarity : 0.004 0.036 1511 Dihedral : 5.283 32.887 1210 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.98 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: 0.05 (0.26), residues: 1055 helix: 0.87 (0.24), residues: 473 sheet: -0.17 (0.59), residues: 77 loop : -0.69 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 247 HIS 0.017 0.002 HIS C 477 PHE 0.023 0.002 PHE A 390 TYR 0.027 0.002 TYR C 534 ARG 0.004 0.001 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8511 (mmm) cc_final: 0.7691 (mmt) REVERT: A 417 LEU cc_start: 0.8882 (mt) cc_final: 0.8538 (pt) REVERT: A 436 GLN cc_start: 0.8405 (tm-30) cc_final: 0.7956 (tm-30) REVERT: A 486 ASP cc_start: 0.8388 (t0) cc_final: 0.7297 (t0) REVERT: A 504 GLN cc_start: 0.8191 (mm110) cc_final: 0.6977 (pm20) REVERT: A 532 TYR cc_start: 0.8787 (t80) cc_final: 0.8522 (t80) REVERT: A 553 ASN cc_start: 0.9102 (t0) cc_final: 0.8797 (t0) REVERT: B 141 ILE cc_start: 0.9189 (mm) cc_final: 0.8964 (mp) REVERT: B 190 ASP cc_start: 0.8580 (t0) cc_final: 0.7750 (t0) REVERT: B 249 MET cc_start: 0.9348 (tmm) cc_final: 0.8888 (tmm) REVERT: B 253 LEU cc_start: 0.9231 (mm) cc_final: 0.8736 (mm) REVERT: B 324 LYS cc_start: 0.6822 (ptpp) cc_final: 0.6082 (mmtt) REVERT: C 412 MET cc_start: 0.5886 (ttt) cc_final: 0.5115 (tmm) REVERT: C 444 GLN cc_start: 0.8858 (mt0) cc_final: 0.8516 (mt0) REVERT: C 458 TYR cc_start: 0.8917 (t80) cc_final: 0.8571 (t80) REVERT: C 469 MET cc_start: 0.9112 (mmm) cc_final: 0.8739 (tpp) REVERT: D 94 MET cc_start: 0.8058 (mpp) cc_final: 0.7798 (mpp) REVERT: D 199 ASN cc_start: 0.9192 (t0) cc_final: 0.8899 (t0) REVERT: D 209 PHE cc_start: 0.9121 (p90) cc_final: 0.8719 (p90) REVERT: D 249 MET cc_start: 0.8693 (ppp) cc_final: 0.8437 (ppp) REVERT: D 314 LEU cc_start: 0.8701 (mp) cc_final: 0.8500 (mp) REVERT: D 343 ILE cc_start: 0.8444 (mt) cc_final: 0.8048 (mt) REVERT: D 378 THR cc_start: 0.7939 (m) cc_final: 0.7542 (p) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1756 time to fit residues: 54.1693 Evaluate side-chains 173 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.097247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.077062 restraints weight = 26326.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.079513 restraints weight = 15021.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.081181 restraints weight = 10225.092| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8861 Z= 0.194 Angle : 0.620 8.104 11952 Z= 0.322 Chirality : 0.046 0.164 1314 Planarity : 0.004 0.033 1511 Dihedral : 5.002 31.237 1210 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.60 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 0.27 (0.26), residues: 1055 helix: 1.02 (0.24), residues: 475 sheet: -0.04 (0.59), residues: 73 loop : -0.54 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 247 HIS 0.008 0.001 HIS D 119 PHE 0.010 0.001 PHE C 390 TYR 0.009 0.001 TYR C 532 ARG 0.003 0.001 ARG A 554 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.8176 (m-80) cc_final: 0.7700 (m-80) REVERT: A 412 MET cc_start: 0.8579 (mmm) cc_final: 0.7759 (mmt) REVERT: A 417 LEU cc_start: 0.8926 (mt) cc_final: 0.8430 (pt) REVERT: A 436 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 441 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8774 (tm-30) REVERT: A 456 MET cc_start: 0.9447 (mmm) cc_final: 0.9067 (mmm) REVERT: A 486 ASP cc_start: 0.8103 (t0) cc_final: 0.7367 (t0) REVERT: A 504 GLN cc_start: 0.8164 (mm110) cc_final: 0.6939 (pm20) REVERT: A 516 VAL cc_start: 0.9590 (t) cc_final: 0.9262 (t) REVERT: A 532 TYR cc_start: 0.8779 (t80) cc_final: 0.8511 (t80) REVERT: A 553 ASN cc_start: 0.9054 (t0) cc_final: 0.8763 (t0) REVERT: B 190 ASP cc_start: 0.8587 (t0) cc_final: 0.7716 (t0) REVERT: B 249 MET cc_start: 0.9352 (tmm) cc_final: 0.8850 (tmm) REVERT: B 253 LEU cc_start: 0.9230 (mm) cc_final: 0.8747 (mm) REVERT: B 308 MET cc_start: 0.4534 (mmp) cc_final: 0.4146 (mmp) REVERT: B 342 LEU cc_start: 0.8146 (mm) cc_final: 0.7779 (mm) REVERT: C 412 MET cc_start: 0.5933 (ttt) cc_final: 0.5332 (tmm) REVERT: C 442 MET cc_start: 0.8747 (mmp) cc_final: 0.7982 (mtp) REVERT: C 444 GLN cc_start: 0.8822 (mt0) cc_final: 0.8468 (mt0) REVERT: C 469 MET cc_start: 0.9139 (mmm) cc_final: 0.8807 (tpp) REVERT: C 560 MET cc_start: 0.8652 (tpp) cc_final: 0.8424 (tpp) REVERT: C 583 ARG cc_start: 0.8488 (tpm170) cc_final: 0.8234 (tpm170) REVERT: D 94 MET cc_start: 0.8046 (mpp) cc_final: 0.7644 (mpp) REVERT: D 111 ILE cc_start: 0.9447 (mt) cc_final: 0.9221 (mm) REVERT: D 209 PHE cc_start: 0.9096 (p90) cc_final: 0.8717 (p90) REVERT: D 249 MET cc_start: 0.8531 (ppp) cc_final: 0.8260 (ppp) REVERT: D 343 ILE cc_start: 0.8270 (mt) cc_final: 0.7869 (mt) REVERT: D 378 THR cc_start: 0.7945 (m) cc_final: 0.7573 (p) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1719 time to fit residues: 56.0453 Evaluate side-chains 185 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 86 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.096918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.076621 restraints weight = 26671.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.079031 restraints weight = 15236.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.080665 restraints weight = 10416.839| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8861 Z= 0.217 Angle : 0.640 8.269 11952 Z= 0.331 Chirality : 0.047 0.194 1314 Planarity : 0.004 0.058 1511 Dihedral : 5.037 31.493 1210 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.70 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 0.24 (0.26), residues: 1055 helix: 1.00 (0.24), residues: 475 sheet: -0.17 (0.58), residues: 77 loop : -0.55 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 247 HIS 0.008 0.001 HIS D 119 PHE 0.022 0.002 PHE A 390 TYR 0.020 0.002 TYR D 316 ARG 0.005 0.001 ARG D 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8621 (mmm) cc_final: 0.7780 (mmt) REVERT: A 436 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7882 (tm-30) REVERT: A 456 MET cc_start: 0.9446 (mmm) cc_final: 0.9077 (mmm) REVERT: A 486 ASP cc_start: 0.8577 (t0) cc_final: 0.7830 (t0) REVERT: A 504 GLN cc_start: 0.8129 (mm110) cc_final: 0.6852 (pm20) REVERT: A 532 TYR cc_start: 0.8821 (t80) cc_final: 0.8500 (t80) REVERT: A 553 ASN cc_start: 0.9071 (t0) cc_final: 0.8816 (t0) REVERT: B 182 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8683 (mm-30) REVERT: B 183 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8623 (ttmt) REVERT: B 190 ASP cc_start: 0.8386 (t0) cc_final: 0.7754 (t0) REVERT: B 229 TYR cc_start: 0.8797 (m-80) cc_final: 0.8560 (m-80) REVERT: B 249 MET cc_start: 0.9367 (tmm) cc_final: 0.8886 (tmm) REVERT: B 253 LEU cc_start: 0.9223 (mm) cc_final: 0.8806 (mm) REVERT: C 412 MET cc_start: 0.5873 (ttt) cc_final: 0.5411 (tmm) REVERT: C 442 MET cc_start: 0.8779 (mmp) cc_final: 0.8020 (mtp) REVERT: C 444 GLN cc_start: 0.8871 (mt0) cc_final: 0.8497 (mt0) REVERT: C 469 MET cc_start: 0.9255 (mmm) cc_final: 0.8786 (tpp) REVERT: C 536 ILE cc_start: 0.9626 (mt) cc_final: 0.9386 (mt) REVERT: C 553 ASN cc_start: 0.8696 (t0) cc_final: 0.8331 (t0) REVERT: C 560 MET cc_start: 0.8696 (tpp) cc_final: 0.8485 (tpp) REVERT: C 577 CYS cc_start: 0.7932 (m) cc_final: 0.7608 (t) REVERT: C 583 ARG cc_start: 0.8534 (tpm170) cc_final: 0.8218 (tpm170) REVERT: D 94 MET cc_start: 0.8092 (mpp) cc_final: 0.7696 (mpp) REVERT: D 111 ILE cc_start: 0.9458 (mt) cc_final: 0.9211 (mm) REVERT: D 199 ASN cc_start: 0.9027 (t0) cc_final: 0.8635 (t0) REVERT: D 209 PHE cc_start: 0.9134 (p90) cc_final: 0.8705 (p90) REVERT: D 249 MET cc_start: 0.8537 (ppp) cc_final: 0.8258 (ppp) REVERT: D 308 MET cc_start: 0.4433 (ptp) cc_final: 0.3799 (ptp) REVERT: D 343 ILE cc_start: 0.8255 (mt) cc_final: 0.7791 (mt) REVERT: D 378 THR cc_start: 0.8004 (m) cc_final: 0.7599 (p) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1677 time to fit residues: 55.2182 Evaluate side-chains 181 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 100 optimal weight: 0.0010 chunk 48 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.099414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.079057 restraints weight = 25835.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.081600 restraints weight = 14421.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.083390 restraints weight = 9675.566| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8861 Z= 0.160 Angle : 0.612 7.875 11952 Z= 0.316 Chirality : 0.046 0.160 1314 Planarity : 0.003 0.038 1511 Dihedral : 4.797 29.849 1210 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.51 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 0.39 (0.26), residues: 1055 helix: 1.17 (0.24), residues: 475 sheet: -0.08 (0.61), residues: 73 loop : -0.52 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 247 HIS 0.007 0.001 HIS D 119 PHE 0.020 0.001 PHE A 390 TYR 0.021 0.001 TYR C 534 ARG 0.003 0.000 ARG A 554 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2748.31 seconds wall clock time: 49 minutes 5.62 seconds (2945.62 seconds total)