Starting phenix.real_space_refine on Sun Dec 29 00:26:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x1w_32951/12_2024/7x1w_32951.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x1w_32951/12_2024/7x1w_32951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x1w_32951/12_2024/7x1w_32951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x1w_32951/12_2024/7x1w_32951.map" model { file = "/net/cci-nas-00/data/ceres_data/7x1w_32951/12_2024/7x1w_32951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x1w_32951/12_2024/7x1w_32951.cif" } resolution = 3.3 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= 0.026 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 P 6 5.49 5 S 44 5.16 5 C 5967 2.51 5 N 1641 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9315 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4624 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 557} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4629 Classifications: {'peptide': 580} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 558} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.60, per 1000 atoms: 0.71 Number of scatterers: 9315 At special positions: 0 Unit cell: (80.51, 83.83, 135.29, 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 44 16.00 P 6 15.00 O 1657 8.00 N 1641 7.00 C 5967 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: 2.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 68.8% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 68 through 83 removed outlier: 3.808A pdb=" N GLN A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 124 removed outlier: 3.649A pdb=" N TYR A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 140 Processing helix chain 'A' and resid 140 through 175 removed outlier: 3.537A pdb=" N ARG A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 186 removed outlier: 4.086A pdb=" N SER A 184 " --> pdb=" O TYR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 236 removed outlier: 3.819A pdb=" N ASP A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) Proline residue: A 218 - end of helix removed outlier: 3.649A pdb=" N TYR A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 255 through 256 No H-bonds generated for 'chain 'A' and resid 255 through 256' Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.536A pdb=" N PHE A 261 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER A 262 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 289 removed outlier: 4.425A pdb=" N GLU A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 298 through 324 removed outlier: 3.572A pdb=" N ALA A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'A' and resid 338 through 353 removed outlier: 3.872A pdb=" N LEU A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 373 through 431 removed outlier: 3.926A pdb=" N SER A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 414 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 521 Processing helix chain 'A' and resid 552 through 556 Processing helix chain 'A' and resid 574 through 583 removed outlier: 4.069A pdb=" N VAL A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 4.273A pdb=" N LEU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN A 590 " --> pdb=" O HIS A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 585 through 590' Processing helix chain 'A' and resid 606 through 622 removed outlier: 4.252A pdb=" N GLN A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG A 612 " --> pdb=" O GLY A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 651 removed outlier: 3.542A pdb=" N LYS A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 667 removed outlier: 4.028A pdb=" N LYS A 665 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS A 667 " --> pdb=" O TRP A 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 83 removed outlier: 3.712A pdb=" N LEU B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 124 removed outlier: 3.645A pdb=" N TYR B 110 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 140 Processing helix chain 'B' and resid 140 through 175 removed outlier: 3.580A pdb=" N ARG B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 186 removed outlier: 4.049A pdb=" N SER B 184 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 198 through 226 removed outlier: 3.623A pdb=" N VAL B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 226 through 236 removed outlier: 3.640A pdb=" N LEU B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 260 Processing helix chain 'B' and resid 263 through 289 removed outlier: 4.088A pdb=" N GLU B 267 " --> pdb=" O PRO B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 297 Processing helix chain 'B' and resid 298 through 337 Processing helix chain 'B' and resid 338 through 354 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 373 through 431 removed outlier: 3.931A pdb=" N SER B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 410 " --> pdb=" O TYR B 406 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 521 Processing helix chain 'B' and resid 572 through 583 removed outlier: 4.051A pdb=" N VAL B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 590 removed outlier: 4.231A pdb=" N LEU B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 590 " --> pdb=" O HIS B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 585 through 590' Processing helix chain 'B' and resid 606 through 622 removed outlier: 4.129A pdb=" N GLN B 611 " --> pdb=" O GLY B 607 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 612 " --> pdb=" O GLY B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 651 removed outlier: 3.855A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 667 removed outlier: 4.219A pdb=" N LYS B 665 " --> pdb=" O SER B 662 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS B 667 " --> pdb=" O TRP B 664 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 469 Processing sheet with id=AA2, first strand: chain 'A' and resid 481 through 482 Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA4, first strand: chain 'B' and resid 466 through 469 Processing sheet with id=AA5, first strand: chain 'B' and resid 481 through 482 removed outlier: 6.659A pdb=" N ILE B 481 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 539 through 540 586 hydrogen bonds defined for protein. 1716 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: 2.55 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3033 1.34 - 1.46: 1597 1.46 - 1.57: 4807 1.57 - 1.69: 12 1.69 - 1.81: 74 Bond restraints: 9523 Sorted by residual: bond pdb=" C2' ATP B 801 " pdb=" C3' ATP B 801 " ideal model delta sigma weight residual 1.531 1.306 0.225 1.20e-02 6.94e+03 3.51e+02 bond pdb=" C2' ATP A 801 " pdb=" C3' ATP A 801 " ideal model delta sigma weight residual 1.531 1.307 0.224 1.20e-02 6.94e+03 3.50e+02 bond pdb=" C4' ATP B 801 " pdb=" O4' ATP B 801 " ideal model delta sigma weight residual 1.444 1.302 0.142 1.10e-02 8.26e+03 1.67e+02 bond pdb=" C4' ATP A 801 " pdb=" O4' ATP A 801 " ideal model delta sigma weight residual 1.444 1.302 0.142 1.10e-02 8.26e+03 1.67e+02 bond pdb=" C6 ATP B 801 " pdb=" N6 ATP B 801 " ideal model delta sigma weight residual 1.337 1.465 -0.128 1.10e-02 8.26e+03 1.35e+02 ... (remaining 9518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 12764 2.89 - 5.79: 116 5.79 - 8.68: 18 8.68 - 11.57: 5 11.57 - 14.46: 4 Bond angle restraints: 12907 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 125.41 14.46 1.00e+00 1.00e+00 2.09e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 125.44 14.43 1.00e+00 1.00e+00 2.08e+02 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 124.21 12.62 1.00e+00 1.00e+00 1.59e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 124.29 12.54 1.00e+00 1.00e+00 1.57e+02 angle pdb=" C5 ATP B 801 " pdb=" C4 ATP B 801 " pdb=" N3 ATP B 801 " ideal model delta sigma weight residual 126.80 117.87 8.93 1.00e+00 1.00e+00 7.98e+01 ... (remaining 12902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 5027 17.73 - 35.46: 544 35.46 - 53.19: 113 53.19 - 70.91: 15 70.91 - 88.64: 12 Dihedral angle restraints: 5711 sinusoidal: 2348 harmonic: 3363 Sorted by residual: dihedral pdb=" CA LYS A 533 " pdb=" C LYS A 533 " pdb=" N PRO A 534 " pdb=" CA PRO A 534 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA LYS B 533 " pdb=" C LYS B 533 " pdb=" N PRO B 534 " pdb=" CA PRO B 534 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA SER A 572 " pdb=" C SER A 572 " pdb=" N GLU A 573 " pdb=" CA GLU A 573 " ideal model delta harmonic sigma weight residual 180.00 154.66 25.34 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 5708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1207 0.054 - 0.107: 193 0.107 - 0.161: 31 0.161 - 0.214: 2 0.214 - 0.268: 2 Chirality restraints: 1435 Sorted by residual: chirality pdb=" C2' ATP A 801 " pdb=" C1' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" O2' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.41 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C2' ATP B 801 " pdb=" C1' ATP B 801 " pdb=" C3' ATP B 801 " pdb=" O2' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.41 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C3' ATP B 801 " pdb=" C2' ATP B 801 " pdb=" C4' ATP B 801 " pdb=" O3' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1432 not shown) Planarity restraints: 1625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 479 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 480 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 480 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 480 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 507 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO B 508 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 508 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 508 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 507 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO A 508 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 508 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 508 " -0.023 5.00e-02 4.00e+02 ... (remaining 1622 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 238 2.71 - 3.26: 9413 3.26 - 3.81: 14904 3.81 - 4.35: 18596 4.35 - 4.90: 32484 Nonbonded interactions: 75635 Sorted by model distance: nonbonded pdb=" OG1 THR B 506 " pdb=" OE1 GLN B 672 " model vdw 2.163 3.040 nonbonded pdb=" O PRO B 508 " pdb=" NZ LYS B 513 " model vdw 2.253 3.120 nonbonded pdb=" O TYR B 547 " pdb=" NH2 ARG B 617 " model vdw 2.290 3.120 nonbonded pdb=" O GLN B 472 " pdb=" OH TYR B 625 " model vdw 2.294 3.040 nonbonded pdb=" O TYR A 547 " pdb=" NH2 ARG A 617 " model vdw 2.295 3.120 ... (remaining 75630 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' selection = (chain 'B' and (resid 64 through 353 or resid 371 through 682 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.870 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: 0.060 Set scattering table: 0.080 Process input model: 24.400 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.007 0.225 9523 Z= 0.409 Angle : 0.764 14.464 12907 Z= 0.506 Chirality : 0.042 0.268 1435 Planarity : 0.004 0.045 1625 Dihedral : 15.415 88.644 3549 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -0.77 (0.25), residues: 1147 helix: 0.80 (0.20), residues: 746 sheet: -2.70 (0.84), residues: 32 loop : -3.15 (0.28), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 326 HIS 0.003 0.001 HIS A 669 PHE 0.026 0.001 PHE B 540 TYR 0.018 0.002 TYR B 541 ARG 0.004 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.095 Fit side-chains REVERT: A 466 GLN cc_start: 0.7903 (mt0) cc_final: 0.6817 (tt0) REVERT: B 466 GLN cc_start: 0.7863 (mt0) cc_final: 0.6880 (tt0) REVERT: B 498 GLU cc_start: 0.7794 (pt0) cc_final: 0.7468 (pt0) REVERT: B 502 HIS cc_start: 0.8669 (m90) cc_final: 0.8351 (m170) REVERT: B 524 TRP cc_start: 0.8488 (m-10) cc_final: 0.8163 (m-10) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2555 time to fit residues: 38.5316 Evaluate side-chains 90 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 289 ASN A 420 HIS A 433 HIS A 659 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9523 Z= 0.297 Angle : 0.612 8.307 12907 Z= 0.312 Chirality : 0.041 0.149 1435 Planarity : 0.004 0.044 1625 Dihedral : 7.605 74.405 1361 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.72 % Allowed : 6.78 % Favored : 92.51 % 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: -0.64 (0.25), residues: 1147 helix: 0.94 (0.19), residues: 759 sheet: -2.46 (0.68), residues: 48 loop : -3.35 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 326 HIS 0.005 0.001 HIS B 299 PHE 0.018 0.001 PHE B 540 TYR 0.016 0.002 TYR A 296 ARG 0.003 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 1.005 Fit side-chains REVERT: A 615 MET cc_start: 0.8423 (mmm) cc_final: 0.8021 (mmt) REVERT: B 200 ASP cc_start: 0.6516 (m-30) cc_final: 0.6259 (m-30) REVERT: B 466 GLN cc_start: 0.7859 (mt0) cc_final: 0.6874 (tt0) REVERT: B 498 GLU cc_start: 0.7836 (pt0) cc_final: 0.7490 (pt0) outliers start: 7 outliers final: 5 residues processed: 96 average time/residue: 0.2542 time to fit residues: 33.5171 Evaluate side-chains 89 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 0.0870 chunk 103 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9523 Z= 0.219 Angle : 0.548 8.540 12907 Z= 0.281 Chirality : 0.039 0.147 1435 Planarity : 0.004 0.043 1625 Dihedral : 6.494 70.358 1361 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.23 % Allowed : 9.34 % Favored : 89.43 % 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: -0.31 (0.26), residues: 1147 helix: 1.21 (0.19), residues: 763 sheet: -2.40 (0.69), residues: 48 loop : -3.34 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 326 HIS 0.004 0.001 HIS B 299 PHE 0.012 0.001 PHE B 540 TYR 0.016 0.001 TYR A 296 ARG 0.002 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 1.028 Fit side-chains REVERT: A 411 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7898 (tm-30) REVERT: A 618 MET cc_start: 0.8021 (tmm) cc_final: 0.7524 (ttt) REVERT: B 200 ASP cc_start: 0.6479 (m-30) cc_final: 0.6219 (m-30) REVERT: B 466 GLN cc_start: 0.7823 (mt0) cc_final: 0.6885 (tt0) REVERT: B 498 GLU cc_start: 0.7753 (pt0) cc_final: 0.7466 (pt0) outliers start: 12 outliers final: 5 residues processed: 101 average time/residue: 0.2436 time to fit residues: 35.0309 Evaluate side-chains 90 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain B residue 429 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 0.4980 chunk 111 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9523 Z= 0.250 Angle : 0.553 7.785 12907 Z= 0.283 Chirality : 0.040 0.148 1435 Planarity : 0.004 0.044 1625 Dihedral : 6.123 65.044 1361 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.46 % Allowed : 11.50 % Favored : 86.04 % 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: -0.21 (0.26), residues: 1147 helix: 1.26 (0.19), residues: 764 sheet: -2.33 (0.71), residues: 48 loop : -3.24 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 326 HIS 0.004 0.001 HIS B 299 PHE 0.009 0.001 PHE B 540 TYR 0.016 0.001 TYR A 296 ARG 0.002 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 1.039 Fit side-chains REVERT: A 163 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7314 (ttt180) REVERT: A 177 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6070 (mm-40) REVERT: A 411 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7794 (tm-30) REVERT: A 618 MET cc_start: 0.8059 (tmm) cc_final: 0.7556 (ttt) REVERT: B 177 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.6101 (mm-40) REVERT: B 466 GLN cc_start: 0.7828 (mt0) cc_final: 0.6879 (tt0) REVERT: B 498 GLU cc_start: 0.7712 (pt0) cc_final: 0.7391 (pt0) REVERT: B 615 MET cc_start: 0.8290 (mmm) cc_final: 0.7875 (mmp) outliers start: 24 outliers final: 14 residues processed: 107 average time/residue: 0.2447 time to fit residues: 36.0949 Evaluate side-chains 100 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 177 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 94 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9523 Z= 0.231 Angle : 0.553 10.564 12907 Z= 0.280 Chirality : 0.040 0.252 1435 Planarity : 0.004 0.044 1625 Dihedral : 5.936 64.728 1361 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.57 % Allowed : 12.73 % Favored : 84.70 % 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: -0.04 (0.26), residues: 1147 helix: 1.39 (0.19), residues: 764 sheet: -2.27 (0.71), residues: 48 loop : -3.16 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 326 HIS 0.005 0.001 HIS B 621 PHE 0.007 0.001 PHE A 385 TYR 0.016 0.001 TYR A 296 ARG 0.002 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 1.118 Fit side-chains REVERT: A 163 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7306 (ttt180) REVERT: A 177 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6030 (mm-40) REVERT: A 178 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7962 (mt0) REVERT: A 200 ASP cc_start: 0.6616 (m-30) cc_final: 0.6368 (m-30) REVERT: A 411 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7731 (tm-30) REVERT: A 618 MET cc_start: 0.8097 (tmm) cc_final: 0.7568 (ttt) REVERT: B 177 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7078 (mt0) REVERT: B 178 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: B 200 ASP cc_start: 0.6511 (m-30) cc_final: 0.6305 (m-30) REVERT: B 466 GLN cc_start: 0.7816 (mt0) cc_final: 0.6891 (tt0) REVERT: B 498 GLU cc_start: 0.7678 (pt0) cc_final: 0.7352 (pt0) REVERT: B 615 MET cc_start: 0.8235 (mmm) cc_final: 0.7881 (mmp) outliers start: 25 outliers final: 16 residues processed: 109 average time/residue: 0.2326 time to fit residues: 35.3780 Evaluate side-chains 101 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 177 GLN Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.0370 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 107 optimal weight: 0.0570 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9523 Z= 0.190 Angle : 0.527 8.731 12907 Z= 0.267 Chirality : 0.039 0.232 1435 Planarity : 0.004 0.043 1625 Dihedral : 5.637 62.652 1361 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.98 % Allowed : 13.45 % Favored : 83.57 % 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: 0.21 (0.26), residues: 1147 helix: 1.60 (0.19), residues: 763 sheet: -1.98 (0.77), residues: 44 loop : -3.12 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 326 HIS 0.003 0.001 HIS B 621 PHE 0.007 0.001 PHE A 385 TYR 0.015 0.001 TYR A 296 ARG 0.002 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 1.034 Fit side-chains REVERT: A 163 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7252 (ttt180) REVERT: A 200 ASP cc_start: 0.6533 (m-30) cc_final: 0.6323 (m-30) REVERT: A 411 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 618 MET cc_start: 0.8080 (tmm) cc_final: 0.7584 (ttt) REVERT: B 200 ASP cc_start: 0.6502 (m-30) cc_final: 0.6270 (m-30) REVERT: B 403 MET cc_start: 0.7703 (mmm) cc_final: 0.7467 (mmp) REVERT: B 466 GLN cc_start: 0.7823 (mt0) cc_final: 0.6899 (tt0) REVERT: B 498 GLU cc_start: 0.7697 (pt0) cc_final: 0.7391 (pt0) REVERT: B 615 MET cc_start: 0.8266 (mmm) cc_final: 0.7857 (mmp) outliers start: 29 outliers final: 19 residues processed: 118 average time/residue: 0.2471 time to fit residues: 40.0522 Evaluate side-chains 104 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 93 optimal weight: 0.1980 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 0.0770 chunk 67 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9523 Z= 0.188 Angle : 0.527 8.162 12907 Z= 0.267 Chirality : 0.039 0.223 1435 Planarity : 0.004 0.042 1625 Dihedral : 5.466 60.766 1361 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.67 % Allowed : 13.76 % Favored : 83.57 % 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: 0.33 (0.26), residues: 1147 helix: 1.68 (0.19), residues: 763 sheet: -1.89 (0.78), residues: 44 loop : -3.07 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 326 HIS 0.005 0.001 HIS A 621 PHE 0.007 0.001 PHE A 385 TYR 0.015 0.001 TYR A 296 ARG 0.002 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 1.021 Fit side-chains REVERT: A 163 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7264 (ttt180) REVERT: A 346 MET cc_start: 0.8108 (mtm) cc_final: 0.7846 (mtp) REVERT: B 200 ASP cc_start: 0.6480 (m-30) cc_final: 0.6245 (m-30) REVERT: B 403 MET cc_start: 0.7663 (mmm) cc_final: 0.7439 (mmp) REVERT: B 466 GLN cc_start: 0.7815 (mt0) cc_final: 0.6909 (tt0) REVERT: B 498 GLU cc_start: 0.7692 (pt0) cc_final: 0.7490 (pt0) REVERT: B 615 MET cc_start: 0.8268 (mmm) cc_final: 0.7861 (mmp) outliers start: 26 outliers final: 21 residues processed: 111 average time/residue: 0.2413 time to fit residues: 37.2744 Evaluate side-chains 105 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9523 Z= 0.254 Angle : 0.560 7.797 12907 Z= 0.284 Chirality : 0.041 0.204 1435 Planarity : 0.004 0.042 1625 Dihedral : 5.547 60.883 1361 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.46 % Allowed : 14.58 % Favored : 82.96 % 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: 0.21 (0.26), residues: 1147 helix: 1.57 (0.19), residues: 763 sheet: -2.13 (0.72), residues: 48 loop : -3.04 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 326 HIS 0.004 0.001 HIS B 299 PHE 0.007 0.001 PHE B 265 TYR 0.019 0.001 TYR A 415 ARG 0.002 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 1.005 Fit side-chains REVERT: A 163 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7392 (ttt180) REVERT: A 346 MET cc_start: 0.8137 (mtm) cc_final: 0.7809 (mtp) REVERT: B 200 ASP cc_start: 0.6502 (m-30) cc_final: 0.6258 (m-30) REVERT: B 376 GLU cc_start: 0.7201 (tt0) cc_final: 0.6968 (mm-30) REVERT: B 403 MET cc_start: 0.7689 (mmm) cc_final: 0.7414 (mmp) REVERT: B 466 GLN cc_start: 0.7833 (mt0) cc_final: 0.6903 (tt0) REVERT: B 498 GLU cc_start: 0.7831 (pt0) cc_final: 0.7537 (pt0) REVERT: B 615 MET cc_start: 0.8217 (mmm) cc_final: 0.7855 (mmm) outliers start: 24 outliers final: 19 residues processed: 99 average time/residue: 0.2355 time to fit residues: 32.4191 Evaluate side-chains 99 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.0470 chunk 106 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9523 Z= 0.228 Angle : 0.551 7.616 12907 Z= 0.279 Chirality : 0.040 0.200 1435 Planarity : 0.004 0.043 1625 Dihedral : 5.498 60.380 1361 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.57 % Allowed : 14.48 % Favored : 82.96 % 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: 1147 helix: 1.61 (0.19), residues: 763 sheet: -1.89 (0.75), residues: 46 loop : -3.03 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 326 HIS 0.003 0.001 HIS B 299 PHE 0.007 0.001 PHE A 385 TYR 0.014 0.001 TYR A 296 ARG 0.002 0.000 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 1.022 Fit side-chains REVERT: A 163 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7322 (ttt180) REVERT: A 346 MET cc_start: 0.8120 (mtm) cc_final: 0.7784 (mtp) REVERT: B 200 ASP cc_start: 0.6493 (m-30) cc_final: 0.6251 (m-30) REVERT: B 376 GLU cc_start: 0.7169 (tt0) cc_final: 0.6879 (mm-30) REVERT: B 403 MET cc_start: 0.7670 (mmm) cc_final: 0.7389 (mmp) REVERT: B 466 GLN cc_start: 0.7835 (mt0) cc_final: 0.6915 (tt0) REVERT: B 498 GLU cc_start: 0.7825 (pt0) cc_final: 0.7560 (pt0) REVERT: B 618 MET cc_start: 0.8073 (tmm) cc_final: 0.7649 (ttt) outliers start: 25 outliers final: 20 residues processed: 99 average time/residue: 0.2130 time to fit residues: 30.4747 Evaluate side-chains 98 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9523 Z= 0.251 Angle : 0.561 7.493 12907 Z= 0.285 Chirality : 0.040 0.193 1435 Planarity : 0.004 0.042 1625 Dihedral : 5.539 60.308 1361 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.16 % Allowed : 15.20 % Favored : 82.65 % 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: 0.21 (0.26), residues: 1147 helix: 1.55 (0.19), residues: 763 sheet: -1.93 (0.74), residues: 46 loop : -2.99 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 326 HIS 0.004 0.001 HIS B 299 PHE 0.007 0.001 PHE A 385 TYR 0.014 0.001 TYR A 296 ARG 0.002 0.000 ARG B 324 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 1.110 Fit side-chains REVERT: A 163 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7335 (ttt180) REVERT: A 346 MET cc_start: 0.8139 (mtm) cc_final: 0.7801 (mtp) REVERT: B 200 ASP cc_start: 0.6507 (m-30) cc_final: 0.6277 (m-30) REVERT: B 376 GLU cc_start: 0.7171 (tt0) cc_final: 0.6883 (mm-30) REVERT: B 466 GLN cc_start: 0.7829 (mt0) cc_final: 0.6893 (tt0) REVERT: B 498 GLU cc_start: 0.7816 (pt0) cc_final: 0.7531 (pt0) outliers start: 21 outliers final: 20 residues processed: 99 average time/residue: 0.2229 time to fit residues: 31.4469 Evaluate side-chains 99 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 0.0770 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.169807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.125909 restraints weight = 9134.707| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.66 r_work: 0.3271 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9523 Z= 0.234 Angle : 0.554 7.486 12907 Z= 0.281 Chirality : 0.040 0.190 1435 Planarity : 0.004 0.042 1625 Dihedral : 5.507 60.056 1361 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.26 % Allowed : 15.09 % Favored : 82.65 % 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: 0.27 (0.26), residues: 1147 helix: 1.58 (0.19), residues: 763 sheet: -1.81 (0.81), residues: 42 loop : -2.96 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 326 HIS 0.004 0.001 HIS B 299 PHE 0.007 0.001 PHE A 385 TYR 0.015 0.001 TYR B 415 ARG 0.002 0.000 ARG B 324 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2173.84 seconds wall clock time: 40 minutes 52.87 seconds (2452.87 seconds total)