Starting phenix.real_space_refine on Wed Sep 25 02:06:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/09_2024/7pru_13610.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/09_2024/7pru_13610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/09_2024/7pru_13610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/09_2024/7pru_13610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/09_2024/7pru_13610.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/09_2024/7pru_13610.cif" } resolution = 3.2 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= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 5836 2.51 5 N 1586 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9116 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4538 Classifications: {'peptide': 582} Link IDs: {'PTRANS': 17, 'TRANS': 564} Chain: "B" Number of atoms: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4538 Classifications: {'peptide': 582} Link IDs: {'PTRANS': 17, 'TRANS': 564} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'GSH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'GSH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.83, per 1000 atoms: 0.86 Number of scatterers: 9116 At special positions: 0 Unit cell: (85.696, 89.856, 139.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1666 8.00 N 1586 7.00 C 5836 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: 2.74 Conformation dependent library (CDL) restraints added in 1.1 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 70.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.889A pdb=" N GLN A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 144 removed outlier: 3.766A pdb=" N VAL A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.812A pdb=" N GLY A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 206 removed outlier: 3.807A pdb=" N GLN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 215 through 240 Processing helix chain 'A' and resid 240 through 260 removed outlier: 3.524A pdb=" N ALA A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 309 removed outlier: 3.812A pdb=" N ALA A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE A 288 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 318 through 372 removed outlier: 3.750A pdb=" N GLU A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 391 removed outlier: 3.962A pdb=" N VAL A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 removed outlier: 3.548A pdb=" N LEU A 397 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 418 removed outlier: 3.712A pdb=" N ARG A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 488 removed outlier: 3.891A pdb=" N ARG A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 530 through 537 Processing helix chain 'A' and resid 543 through 554 removed outlier: 3.638A pdb=" N VAL A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 562 Processing helix chain 'A' and resid 565 through 569 Processing helix chain 'A' and resid 579 through 595 Processing helix chain 'A' and resid 610 through 625 Processing helix chain 'A' and resid 660 through 665 Processing helix chain 'A' and resid 670 through 674 removed outlier: 4.443A pdb=" N GLU A 673 " --> pdb=" O VAL A 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 105 Processing helix chain 'B' and resid 109 through 144 removed outlier: 3.767A pdb=" N VAL B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 154 through 160 removed outlier: 3.812A pdb=" N GLY B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 206 removed outlier: 3.807A pdb=" N GLN B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 215 through 240 Processing helix chain 'B' and resid 240 through 260 removed outlier: 3.523A pdb=" N ALA B 245 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 309 removed outlier: 3.811A pdb=" N ALA B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 318 through 372 removed outlier: 3.750A pdb=" N GLU B 322 " --> pdb=" O ASN B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 391 removed outlier: 3.962A pdb=" N VAL B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 3.549A pdb=" N LEU B 397 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 418 removed outlier: 3.712A pdb=" N ARG B 402 " --> pdb=" O GLY B 398 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 488 removed outlier: 3.892A pdb=" N ARG B 485 " --> pdb=" O SER B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 530 through 537 Processing helix chain 'B' and resid 543 through 554 removed outlier: 3.638A pdb=" N VAL B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 562 Processing helix chain 'B' and resid 565 through 569 Processing helix chain 'B' and resid 579 through 595 Processing helix chain 'B' and resid 610 through 625 Processing helix chain 'B' and resid 660 through 665 Processing helix chain 'B' and resid 670 through 674 removed outlier: 4.444A pdb=" N GLU B 673 " --> pdb=" O VAL B 670 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 457 through 464 removed outlier: 4.862A pdb=" N ARG A 458 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE A 448 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU A 462 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU A 444 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE A 464 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ARG A 442 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE A 443 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE A 499 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASN A 445 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LYS A 497 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 517 through 520 removed outlier: 6.594A pdb=" N GLY A 518 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASP A 602 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL A 520 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 599 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A 634 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE A 601 " --> pdb=" O VAL A 634 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 470 " --> pdb=" O PHE A 633 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LYS A 469 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE A 648 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA A 471 " --> pdb=" O ILE A 648 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU A 650 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 473 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 647 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN A 658 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 649 " --> pdb=" O VAL A 656 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 457 through 464 removed outlier: 4.863A pdb=" N ARG B 458 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE B 448 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU B 462 " --> pdb=" O GLU B 444 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU B 444 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE B 464 " --> pdb=" O ARG B 442 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ARG B 442 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE B 443 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE B 499 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASN B 445 " --> pdb=" O LYS B 497 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS B 497 " --> pdb=" O ASN B 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 517 through 520 removed outlier: 6.593A pdb=" N GLY B 518 " --> pdb=" O PHE B 600 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASP B 602 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 520 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 599 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL B 634 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE B 601 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 470 " --> pdb=" O PHE B 633 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LYS B 469 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE B 648 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA B 471 " --> pdb=" O ILE B 648 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU B 650 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL B 473 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE B 647 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN B 658 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 649 " --> pdb=" O VAL B 656 " (cutoff:3.500A) 592 hydrogen bonds defined for protein. 1722 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: 2.89 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1484 1.30 - 1.43: 2404 1.43 - 1.56: 5344 1.56 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 9282 Sorted by residual: bond pdb=" CD1 GSH B 801 " pdb=" N2 GSH B 801 " ideal model delta sigma weight residual 1.336 1.453 -0.117 1.20e-02 6.94e+03 9.51e+01 bond pdb=" CD1 GSH A 801 " pdb=" N2 GSH A 801 " ideal model delta sigma weight residual 1.336 1.451 -0.115 1.20e-02 6.94e+03 9.15e+01 bond pdb=" C2 GSH A 801 " pdb=" N3 GSH A 801 " ideal model delta sigma weight residual 1.333 1.449 -0.116 1.30e-02 5.92e+03 7.92e+01 bond pdb=" C2 GSH B 801 " pdb=" N3 GSH B 801 " ideal model delta sigma weight residual 1.333 1.448 -0.115 1.30e-02 5.92e+03 7.86e+01 bond pdb=" C2 GSH A 801 " pdb=" O2 GSH A 801 " ideal model delta sigma weight residual 1.227 1.181 0.046 1.00e-02 1.00e+04 2.13e+01 ... (remaining 9277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 11738 1.90 - 3.80: 698 3.80 - 5.70: 111 5.70 - 7.60: 26 7.60 - 9.50: 11 Bond angle restraints: 12584 Sorted by residual: angle pdb=" CG1 GSH B 801 " pdb=" CD1 GSH B 801 " pdb=" N2 GSH B 801 " ideal model delta sigma weight residual 115.92 121.70 -5.78 1.00e+00 1.00e+00 3.35e+01 angle pdb=" CG1 GSH A 801 " pdb=" CD1 GSH A 801 " pdb=" N2 GSH A 801 " ideal model delta sigma weight residual 115.92 121.06 -5.14 1.00e+00 1.00e+00 2.64e+01 angle pdb=" SG2 GSH B 801 " pdb=" CB2 GSH B 801 " pdb=" CA2 GSH B 801 " ideal model delta sigma weight residual 114.04 109.81 4.23 1.00e+00 1.00e+00 1.79e+01 angle pdb=" N PHE B 355 " pdb=" CA PHE B 355 " pdb=" CB PHE B 355 " ideal model delta sigma weight residual 110.22 115.78 -5.56 1.54e+00 4.22e-01 1.30e+01 angle pdb=" CA3 GSH A 801 " pdb=" C3 GSH A 801 " pdb=" O32 GSH A 801 " ideal model delta sigma weight residual 111.89 120.66 -8.77 2.43e+00 1.69e-01 1.30e+01 ... (remaining 12579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 4988 17.42 - 34.84: 456 34.84 - 52.27: 96 52.27 - 69.69: 21 69.69 - 87.11: 13 Dihedral angle restraints: 5574 sinusoidal: 2202 harmonic: 3372 Sorted by residual: dihedral pdb=" CA ASN A 421 " pdb=" C ASN A 421 " pdb=" N VAL A 422 " pdb=" CA VAL A 422 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASN B 421 " pdb=" C ASN B 421 " pdb=" N VAL B 422 " pdb=" CA VAL B 422 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ARG B 102 " pdb=" C ARG B 102 " pdb=" N TYR B 103 " pdb=" CA TYR B 103 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 5571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1147 0.068 - 0.136: 280 0.136 - 0.203: 34 0.203 - 0.271: 9 0.271 - 0.339: 2 Chirality restraints: 1472 Sorted by residual: chirality pdb=" CA PHE A 355 " pdb=" N PHE A 355 " pdb=" C PHE A 355 " pdb=" CB PHE A 355 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA PHE B 355 " pdb=" N PHE B 355 " pdb=" C PHE B 355 " pdb=" CB PHE B 355 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB VAL B 571 " pdb=" CA VAL B 571 " pdb=" CG1 VAL B 571 " pdb=" CG2 VAL B 571 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 1469 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 431 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.94e+00 pdb=" N PRO A 432 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 432 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 432 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 431 " -0.043 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO B 432 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 388 " 0.026 2.00e-02 2.50e+03 1.82e-02 5.83e+00 pdb=" CG PHE B 388 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE B 388 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 388 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B 388 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 388 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE B 388 " 0.007 2.00e-02 2.50e+03 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 246 2.68 - 3.24: 9396 3.24 - 3.79: 14982 3.79 - 4.35: 18834 4.35 - 4.90: 31789 Nonbonded interactions: 75247 Sorted by model distance: nonbonded pdb=" OD1 ASP A 327 " pdb=" OG1 THR B 197 " model vdw 2.128 3.040 nonbonded pdb=" O ARG A 637 " pdb=" OG1 THR A 640 " model vdw 2.169 3.040 nonbonded pdb=" O ARG B 637 " pdb=" OG1 THR B 640 " model vdw 2.170 3.040 nonbonded pdb=" OH TYR B 274 " pdb=" O LEU B 394 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR A 274 " pdb=" O LEU A 394 " model vdw 2.215 3.040 ... (remaining 75242 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' } 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.120 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.010 0.117 9282 Z= 0.615 Angle : 1.051 9.502 12584 Z= 0.594 Chirality : 0.060 0.339 1472 Planarity : 0.007 0.066 1598 Dihedral : 14.865 87.110 3402 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % 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: -2.01 (0.23), residues: 1160 helix: -0.88 (0.17), residues: 756 sheet: -1.02 (0.60), residues: 74 loop : -2.13 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 110 HIS 0.005 0.002 HIS B 202 PHE 0.035 0.004 PHE A 388 TYR 0.028 0.003 TYR A 274 ARG 0.020 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 SER cc_start: 0.8669 (t) cc_final: 0.8425 (p) REVERT: A 546 GLN cc_start: 0.7373 (mp10) cc_final: 0.7125 (mp10) REVERT: B 537 TYR cc_start: 0.8556 (t80) cc_final: 0.8257 (t80) REVERT: B 599 LEU cc_start: 0.7591 (mp) cc_final: 0.7373 (mp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2416 time to fit residues: 35.2107 Evaluate side-chains 92 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN B 584 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9282 Z= 0.205 Angle : 0.648 7.446 12584 Z= 0.337 Chirality : 0.042 0.164 1472 Planarity : 0.005 0.038 1598 Dihedral : 7.503 76.747 1306 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.52 % Allowed : 7.25 % Favored : 92.24 % 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 (0.24), residues: 1160 helix: 0.26 (0.18), residues: 756 sheet: -0.91 (0.64), residues: 74 loop : -2.09 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.002 0.001 HIS A 611 PHE 0.025 0.002 PHE A 388 TYR 0.021 0.002 TYR A 232 ARG 0.004 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8146 (mttm) REVERT: A 617 MET cc_start: 0.9049 (mmm) cc_final: 0.8778 (mtp) REVERT: B 497 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8293 (mttm) REVERT: B 537 TYR cc_start: 0.8437 (t80) cc_final: 0.8143 (t80) REVERT: B 599 LEU cc_start: 0.7746 (mp) cc_final: 0.7494 (mp) outliers start: 5 outliers final: 5 residues processed: 105 average time/residue: 0.2551 time to fit residues: 36.3341 Evaluate side-chains 98 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 105 optimal weight: 0.3980 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN A 603 GLN B 539 ASN B 603 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9282 Z= 0.248 Angle : 0.631 7.233 12584 Z= 0.326 Chirality : 0.043 0.157 1472 Planarity : 0.004 0.031 1598 Dihedral : 7.054 82.671 1306 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.45 % Allowed : 10.97 % Favored : 87.58 % 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 (0.25), residues: 1160 helix: 0.57 (0.18), residues: 766 sheet: -0.84 (0.66), residues: 74 loop : -2.00 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.002 0.001 HIS A 636 PHE 0.024 0.002 PHE B 388 TYR 0.018 0.002 TYR A 232 ARG 0.004 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.990 Fit side-chains REVERT: A 431 LYS cc_start: 0.8234 (mmtm) cc_final: 0.7817 (mmtp) REVERT: A 497 LYS cc_start: 0.8480 (mmtt) cc_final: 0.8143 (mttm) REVERT: B 497 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8273 (mttp) REVERT: B 537 TYR cc_start: 0.8387 (t80) cc_final: 0.8056 (t80) outliers start: 14 outliers final: 13 residues processed: 105 average time/residue: 0.2315 time to fit residues: 33.6497 Evaluate side-chains 102 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 630 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 70 optimal weight: 0.0060 chunk 105 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9282 Z= 0.220 Angle : 0.606 7.227 12584 Z= 0.311 Chirality : 0.042 0.156 1472 Planarity : 0.004 0.031 1598 Dihedral : 6.755 83.886 1306 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.59 % Allowed : 12.22 % Favored : 85.20 % 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: -0.03 (0.25), residues: 1160 helix: 0.87 (0.19), residues: 758 sheet: -0.74 (0.67), residues: 74 loop : -1.89 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 284 HIS 0.002 0.001 HIS A 636 PHE 0.021 0.002 PHE B 388 TYR 0.018 0.001 TYR A 232 ARG 0.004 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 362 MET cc_start: 0.8007 (mtt) cc_final: 0.7800 (mtt) REVERT: A 497 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8300 (mttm) REVERT: B 497 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8108 (mttm) REVERT: B 537 TYR cc_start: 0.8389 (t80) cc_final: 0.8063 (t80) REVERT: B 617 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8322 (mtt) REVERT: B 623 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8377 (p) outliers start: 25 outliers final: 15 residues processed: 109 average time/residue: 0.2170 time to fit residues: 33.2165 Evaluate side-chains 102 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 630 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9282 Z= 0.219 Angle : 0.596 7.185 12584 Z= 0.306 Chirality : 0.042 0.162 1472 Planarity : 0.004 0.030 1598 Dihedral : 6.670 85.073 1306 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.38 % Allowed : 13.46 % Favored : 84.16 % 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: 0.18 (0.25), residues: 1160 helix: 1.04 (0.19), residues: 758 sheet: -0.42 (0.67), residues: 76 loop : -1.90 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 284 HIS 0.002 0.000 HIS B 636 PHE 0.019 0.002 PHE A 388 TYR 0.018 0.001 TYR B 232 ARG 0.006 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 352 ASN cc_start: 0.8338 (t0) cc_final: 0.7912 (t0) REVERT: A 497 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8293 (mttm) REVERT: A 617 MET cc_start: 0.9032 (mmm) cc_final: 0.8809 (mtp) REVERT: B 100 MET cc_start: 0.5471 (mtt) cc_final: 0.5241 (mtt) REVERT: B 352 ASN cc_start: 0.8357 (t0) cc_final: 0.7905 (t0) REVERT: B 355 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7897 (t80) REVERT: B 537 TYR cc_start: 0.8382 (t80) cc_final: 0.8057 (t80) REVERT: B 664 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6263 (mm) outliers start: 23 outliers final: 17 residues processed: 105 average time/residue: 0.2228 time to fit residues: 33.3086 Evaluate side-chains 101 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9282 Z= 0.352 Angle : 0.656 8.145 12584 Z= 0.337 Chirality : 0.045 0.163 1472 Planarity : 0.004 0.030 1598 Dihedral : 6.874 84.634 1306 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.59 % Allowed : 13.98 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1160 helix: 0.84 (0.19), residues: 762 sheet: -0.73 (0.65), residues: 74 loop : -1.86 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.002 0.001 HIS A 565 PHE 0.024 0.002 PHE A 388 TYR 0.022 0.002 TYR A 274 ARG 0.006 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 355 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7812 (t80) REVERT: A 362 MET cc_start: 0.8098 (mtt) cc_final: 0.7763 (mtt) REVERT: A 497 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8233 (mttm) REVERT: A 617 MET cc_start: 0.9040 (mmm) cc_final: 0.8792 (mtp) REVERT: B 355 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7878 (t80) REVERT: B 497 LYS cc_start: 0.8595 (mttp) cc_final: 0.8261 (mttm) REVERT: B 537 TYR cc_start: 0.8424 (t80) cc_final: 0.8082 (t80) REVERT: B 664 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6343 (mm) outliers start: 25 outliers final: 20 residues processed: 104 average time/residue: 0.2183 time to fit residues: 31.9962 Evaluate side-chains 105 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 0.0040 chunk 44 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN B 621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9282 Z= 0.183 Angle : 0.586 7.054 12584 Z= 0.298 Chirality : 0.041 0.171 1472 Planarity : 0.003 0.029 1598 Dihedral : 6.608 85.080 1306 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.90 % Allowed : 14.39 % Favored : 82.71 % 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 (0.25), residues: 1160 helix: 1.18 (0.19), residues: 758 sheet: -0.29 (0.66), residues: 76 loop : -1.82 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.002 0.000 HIS B 636 PHE 0.018 0.001 PHE B 388 TYR 0.018 0.001 TYR A 232 ARG 0.006 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 87 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ASN cc_start: 0.8293 (t0) cc_final: 0.7897 (t0) REVERT: A 355 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7803 (t80) REVERT: A 362 MET cc_start: 0.7960 (mtt) cc_final: 0.7704 (mtm) REVERT: A 617 MET cc_start: 0.9000 (mmm) cc_final: 0.8785 (mtp) REVERT: B 352 ASN cc_start: 0.8268 (t0) cc_final: 0.7880 (t0) REVERT: B 355 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7806 (t80) REVERT: B 537 TYR cc_start: 0.8397 (t80) cc_final: 0.8064 (t80) REVERT: B 664 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6293 (mm) outliers start: 28 outliers final: 17 residues processed: 111 average time/residue: 0.2123 time to fit residues: 33.2313 Evaluate side-chains 104 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.0070 chunk 10 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 chunk 104 optimal weight: 10.0000 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9282 Z= 0.166 Angle : 0.578 7.757 12584 Z= 0.293 Chirality : 0.041 0.178 1472 Planarity : 0.003 0.029 1598 Dihedral : 6.579 87.993 1306 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.48 % Allowed : 15.84 % Favored : 81.68 % 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: 1160 helix: 1.32 (0.19), residues: 772 sheet: -0.21 (0.67), residues: 76 loop : -1.67 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 284 HIS 0.003 0.000 HIS A 555 PHE 0.012 0.001 PHE B 388 TYR 0.018 0.001 TYR A 232 ARG 0.007 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ASN cc_start: 0.8239 (t0) cc_final: 0.7841 (t0) REVERT: A 355 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7827 (t80) REVERT: A 484 LEU cc_start: 0.8570 (tt) cc_final: 0.8365 (pp) REVERT: A 664 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.6030 (mm) REVERT: B 130 ASN cc_start: 0.8164 (t0) cc_final: 0.7828 (t0) REVERT: B 352 ASN cc_start: 0.8225 (t0) cc_final: 0.7840 (t0) REVERT: B 355 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7827 (t80) REVERT: B 484 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8251 (pp) REVERT: B 537 TYR cc_start: 0.8398 (t80) cc_final: 0.8028 (t80) REVERT: B 664 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6198 (mm) outliers start: 24 outliers final: 16 residues processed: 108 average time/residue: 0.2131 time to fit residues: 32.4728 Evaluate side-chains 105 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9282 Z= 0.233 Angle : 0.620 9.220 12584 Z= 0.311 Chirality : 0.043 0.201 1472 Planarity : 0.003 0.029 1598 Dihedral : 6.590 89.162 1306 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.69 % Allowed : 15.42 % Favored : 81.88 % 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: 0.59 (0.25), residues: 1160 helix: 1.28 (0.19), residues: 772 sheet: -0.29 (0.66), residues: 76 loop : -1.63 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.002 0.001 HIS A 555 PHE 0.016 0.002 PHE B 388 TYR 0.017 0.001 TYR A 232 ARG 0.007 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 84 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ASN cc_start: 0.8241 (t0) cc_final: 0.7622 (t0) REVERT: A 355 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7835 (t80) REVERT: A 362 MET cc_start: 0.7912 (mtt) cc_final: 0.7636 (mtm) REVERT: A 389 GLN cc_start: 0.7518 (mt0) cc_final: 0.7290 (mt0) REVERT: A 497 LYS cc_start: 0.8842 (mttp) cc_final: 0.8641 (mttm) REVERT: A 664 LEU cc_start: 0.6249 (OUTLIER) cc_final: 0.5898 (mm) REVERT: B 130 ASN cc_start: 0.8246 (t0) cc_final: 0.7861 (t0) REVERT: B 355 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7810 (t80) REVERT: B 362 MET cc_start: 0.8043 (mtt) cc_final: 0.7818 (mtt) REVERT: B 484 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8270 (pp) REVERT: B 537 TYR cc_start: 0.8404 (t80) cc_final: 0.8023 (t80) REVERT: B 664 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6251 (mm) outliers start: 26 outliers final: 21 residues processed: 107 average time/residue: 0.2092 time to fit residues: 31.8340 Evaluate side-chains 110 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 84 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 115 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9282 Z= 0.212 Angle : 0.630 15.751 12584 Z= 0.314 Chirality : 0.043 0.278 1472 Planarity : 0.003 0.033 1598 Dihedral : 6.487 89.220 1306 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.69 % Allowed : 16.36 % Favored : 80.95 % 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: 0.63 (0.25), residues: 1160 helix: 1.34 (0.19), residues: 768 sheet: -0.29 (0.67), residues: 76 loop : -1.67 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.002 0.000 HIS A 636 PHE 0.014 0.001 PHE B 388 TYR 0.017 0.001 TYR A 232 ARG 0.008 0.000 ARG A 485 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 86 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASN cc_start: 0.8175 (t0) cc_final: 0.7777 (t0) REVERT: A 355 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7821 (t80) REVERT: A 362 MET cc_start: 0.7897 (mtt) cc_final: 0.7644 (mtm) REVERT: A 664 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5852 (mm) REVERT: B 130 ASN cc_start: 0.8249 (t0) cc_final: 0.7844 (t0) REVERT: B 355 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7779 (t80) REVERT: B 362 MET cc_start: 0.8015 (mtt) cc_final: 0.7790 (mtt) REVERT: B 484 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8297 (pp) REVERT: B 537 TYR cc_start: 0.8389 (t80) cc_final: 0.8006 (t80) REVERT: B 664 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6227 (mm) outliers start: 26 outliers final: 19 residues processed: 108 average time/residue: 0.2164 time to fit residues: 32.9961 Evaluate side-chains 108 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.204023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.129123 restraints weight = 10084.597| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.98 r_work: 0.3423 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9282 Z= 0.193 Angle : 0.595 9.215 12584 Z= 0.298 Chirality : 0.042 0.172 1472 Planarity : 0.003 0.033 1598 Dihedral : 6.376 89.961 1306 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.48 % Allowed : 16.56 % Favored : 80.95 % 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: 1160 helix: 1.45 (0.19), residues: 772 sheet: -0.26 (0.67), residues: 76 loop : -1.66 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.002 0.000 HIS A 636 PHE 0.012 0.001 PHE A 601 TYR 0.018 0.001 TYR A 232 ARG 0.008 0.000 ARG A 485 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2125.69 seconds wall clock time: 42 minutes 47.35 seconds (2567.35 seconds total)