Starting phenix.real_space_refine on Wed Sep 25 14:25:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/09_2024/7oto_13063.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/09_2024/7oto_13063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/09_2024/7oto_13063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/09_2024/7oto_13063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/09_2024/7oto_13063.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/09_2024/7oto_13063.cif" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.006 sd= 0.023 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 51 5.16 5 C 6472 2.51 5 N 1841 2.21 5 O 1961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10333 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4697 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 25, 'TRANS': 576} Chain breaks: 1 Chain: "A" Number of atoms: 5572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5572 Classifications: {'peptide': 711} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 679} Chain breaks: 3 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.27, per 1000 atoms: 0.61 Number of scatterers: 10333 At special positions: 0 Unit cell: (112.36, 121.9, 97.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 6 15.00 Mg 2 11.99 O 1961 8.00 N 1841 7.00 C 6472 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: 2.44 Conformation dependent library (CDL) restraints added in 1.4 seconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 8 sheets defined 55.3% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.720A pdb=" N LEU B 189 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 205 through 218 Processing helix chain 'B' and resid 230 through 248 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 317 through 331 removed outlier: 3.732A pdb=" N LEU B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 346 Proline residue: B 340 - end of helix removed outlier: 3.655A pdb=" N GLY B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 357 Processing helix chain 'B' and resid 361 through 385 Proline residue: B 376 - end of helix removed outlier: 3.811A pdb=" N THR B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 398 removed outlier: 3.578A pdb=" N GLY B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 512 through 536 Processing helix chain 'B' and resid 538 through 566 Processing helix chain 'B' and resid 585 through 592 removed outlier: 4.078A pdb=" N GLN B 590 " --> pdb=" O PRO B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 636 Processing helix chain 'B' and resid 668 through 684 Processing helix chain 'B' and resid 700 through 718 Processing helix chain 'B' and resid 731 through 733 No H-bonds generated for 'chain 'B' and resid 731 through 733' Processing helix chain 'B' and resid 734 through 739 removed outlier: 4.036A pdb=" N LYS B 738 " --> pdb=" O GLN B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 780 Processing helix chain 'B' and resid 782 through 799 Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 41 through 52 removed outlier: 3.617A pdb=" N LYS A 45 " --> pdb=" O TYR A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 87 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 230 through 249 Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 334 through 346 Proline residue: A 340 - end of helix removed outlier: 3.532A pdb=" N GLN A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.622A pdb=" N ILE A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 385 Proline residue: A 376 - end of helix removed outlier: 3.525A pdb=" N THR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.642A pdb=" N GLY A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 430 through 442 Processing helix chain 'A' and resid 513 through 536 Processing helix chain 'A' and resid 538 through 566 Processing helix chain 'A' and resid 585 through 592 removed outlier: 3.808A pdb=" N GLN A 590 " --> pdb=" O PRO A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 635 removed outlier: 3.588A pdb=" N THR A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 684 Processing helix chain 'A' and resid 700 through 718 Processing helix chain 'A' and resid 729 through 733 Processing helix chain 'A' and resid 734 through 739 removed outlier: 3.624A pdb=" N LYS A 738 " --> pdb=" O GLN A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 780 Processing helix chain 'A' and resid 782 through 800 Processing sheet with id=AA1, first strand: chain 'B' and resid 132 through 138 removed outlier: 3.504A pdb=" N ARG B 154 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 178 through 181 removed outlier: 5.894A pdb=" N LEU B 178 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ARG B 199 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N TYR B 180 " --> pdb=" O ARG B 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 570 through 572 removed outlier: 3.637A pdb=" N LYS B 644 " --> pdb=" O THR B 581 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU B 582 " --> pdb=" O ASN B 599 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN B 599 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 653 through 656 removed outlier: 6.222A pdb=" N PHE B 654 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASP B 693 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG B 656 " --> pdb=" O ASP B 693 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 610 " --> pdb=" O PHE B 725 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N MET B 609 " --> pdb=" O ALA B 743 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL B 745 " --> pdb=" O MET B 609 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE B 611 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU B 747 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR B 613 " --> pdb=" O LEU B 747 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ALA B 749 " --> pdb=" O THR B 613 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER B 761 " --> pdb=" O ASP B 748 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N LEU B 750 " --> pdb=" O MET B 759 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET B 759 " --> pdb=" O LEU B 750 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 56 through 58 removed outlier: 5.224A pdb=" N PHE A 40 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU A 29 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 112 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU A 94 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL A 110 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.325A pdb=" N LEU A 178 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ARG A 199 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR A 180 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA A 181 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLN A 138 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 571 through 572 removed outlier: 6.305A pdb=" N THR A 571 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 644 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU A 582 " --> pdb=" O ASN A 599 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASN A 599 " --> pdb=" O GLU A 582 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 653 through 656 removed outlier: 6.136A pdb=" N PHE A 654 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASP A 693 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG A 656 " --> pdb=" O ASP A 693 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N MET A 609 " --> pdb=" O ALA A 743 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL A 745 " --> pdb=" O MET A 609 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE A 611 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU A 747 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASN A 744 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLN A 763 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS A 746 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER A 761 " --> pdb=" O HIS A 746 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP A 748 " --> pdb=" O MET A 759 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1641 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: 3.32 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1765 1.31 - 1.44: 2562 1.44 - 1.57: 6071 1.57 - 1.69: 10 1.69 - 1.82: 91 Bond restraints: 10499 Sorted by residual: bond pdb=" N3B ANP A1002 " pdb=" PG ANP A1002 " ideal model delta sigma weight residual 1.795 1.620 0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" N3B ANP B1002 " pdb=" PG ANP B1002 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.68e+01 bond pdb=" O3A ANP B1002 " pdb=" PB ANP B1002 " ideal model delta sigma weight residual 1.700 1.596 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O3A ANP A1002 " pdb=" PB ANP A1002 " ideal model delta sigma weight residual 1.700 1.600 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ILE A 66 " pdb=" CA ILE A 66 " ideal model delta sigma weight residual 1.458 1.493 -0.035 7.70e-03 1.69e+04 2.07e+01 ... (remaining 10494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 12438 2.83 - 5.66: 1735 5.66 - 8.49: 49 8.49 - 11.32: 4 11.32 - 14.15: 1 Bond angle restraints: 14227 Sorted by residual: angle pdb=" CA GLY B 422 " pdb=" C GLY B 422 " pdb=" O GLY B 422 " ideal model delta sigma weight residual 122.45 117.11 5.34 7.20e-01 1.93e+00 5.50e+01 angle pdb=" CA PHE A 725 " pdb=" CB PHE A 725 " pdb=" CG PHE A 725 " ideal model delta sigma weight residual 113.80 120.50 -6.70 1.00e+00 1.00e+00 4.49e+01 angle pdb=" N PRO A 25 " pdb=" CA PRO A 25 " pdb=" C PRO A 25 " ideal model delta sigma weight residual 113.40 121.99 -8.59 1.34e+00 5.57e-01 4.11e+01 angle pdb=" CA SER B 604 " pdb=" C SER B 604 " pdb=" N PRO B 605 " ideal model delta sigma weight residual 117.68 122.22 -4.54 7.10e-01 1.98e+00 4.09e+01 angle pdb=" C PRO B 231 " pdb=" CA PRO B 231 " pdb=" CB PRO B 231 " ideal model delta sigma weight residual 113.06 102.93 10.13 1.59e+00 3.96e-01 4.06e+01 ... (remaining 14222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.08: 6265 32.08 - 64.17: 176 64.17 - 96.25: 32 96.25 - 128.34: 1 128.34 - 160.42: 1 Dihedral angle restraints: 6475 sinusoidal: 2676 harmonic: 3799 Sorted by residual: dihedral pdb=" O1A ANP B1002 " pdb=" O3A ANP B1002 " pdb=" PA ANP B1002 " pdb=" PB ANP B1002 " ideal model delta sinusoidal sigma weight residual 83.11 -77.31 160.42 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" O1A ANP A1002 " pdb=" O3A ANP A1002 " pdb=" PA ANP A1002 " pdb=" PB ANP A1002 " ideal model delta sinusoidal sigma weight residual 83.11 -39.51 122.62 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C GLN B 248 " pdb=" N GLN B 248 " pdb=" CA GLN B 248 " pdb=" CB GLN B 248 " ideal model delta harmonic sigma weight residual -122.60 -113.29 -9.31 0 2.50e+00 1.60e-01 1.39e+01 ... (remaining 6472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 805 0.075 - 0.149: 540 0.149 - 0.224: 215 0.224 - 0.299: 68 0.299 - 0.373: 2 Chirality restraints: 1630 Sorted by residual: chirality pdb=" CB ILE B 258 " pdb=" CA ILE B 258 " pdb=" CG1 ILE B 258 " pdb=" CG2 ILE B 258 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C3' ANP A1002 " pdb=" C2' ANP A1002 " pdb=" C4' ANP A1002 " pdb=" O3' ANP A1002 " both_signs ideal model delta sigma weight residual False -2.36 -2.72 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA ILE B 258 " pdb=" N ILE B 258 " pdb=" C ILE B 258 " pdb=" CB ILE B 258 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1627 not shown) Planarity restraints: 1852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 268 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.23e+00 pdb=" C ILE B 268 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE B 268 " 0.017 2.00e-02 2.50e+03 pdb=" N MET B 269 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 675 " -0.011 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C THR B 675 " 0.041 2.00e-02 2.50e+03 pdb=" O THR B 675 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU B 676 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 213 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C LEU B 213 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU B 213 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN B 214 " -0.014 2.00e-02 2.50e+03 ... (remaining 1849 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 4 2.42 - 3.04: 5531 3.04 - 3.66: 15957 3.66 - 4.28: 22989 4.28 - 4.90: 39179 Nonbonded interactions: 83660 Sorted by model distance: nonbonded pdb=" OG SER A 621 " pdb="MG MG A1001 " model vdw 1.799 2.170 nonbonded pdb=" OG SER B 621 " pdb="MG MG B1001 " model vdw 2.036 2.170 nonbonded pdb="MG MG A1001 " pdb=" O2B ANP A1002 " model vdw 2.128 2.170 nonbonded pdb="MG MG B1001 " pdb=" O1G ANP B1002 " model vdw 2.273 2.170 nonbonded pdb=" N ASP A 139 " pdb=" O ASP A 139 " model vdw 2.439 2.496 ... (remaining 83655 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.230 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: 0.080 Set scattering table: 0.100 Process input model: 25.560 Find NCS groups from input model: 0.100 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 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 : 0.013 0.175 10499 Z= 0.833 Angle : 1.836 14.147 14227 Z= 1.411 Chirality : 0.110 0.373 1630 Planarity : 0.006 0.034 1852 Dihedral : 15.716 160.421 4017 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % 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: 2.59 (0.21), residues: 1301 helix: 3.35 (0.17), residues: 662 sheet: 0.72 (0.39), residues: 159 loop : -0.34 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 202 HIS 0.010 0.002 HIS B 752 PHE 0.029 0.005 PHE B 532 TYR 0.035 0.003 TYR A 31 ARG 0.007 0.001 ARG B 607 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 147 THR cc_start: 0.8305 (t) cc_final: 0.8057 (m) REVERT: B 197 ARG cc_start: 0.7617 (mtp85) cc_final: 0.7328 (mtp180) REVERT: B 198 ARG cc_start: 0.7980 (mtm110) cc_final: 0.7511 (mtm-85) REVERT: B 201 LEU cc_start: 0.8205 (tp) cc_final: 0.7935 (mm) REVERT: B 205 GLU cc_start: 0.7437 (tt0) cc_final: 0.7155 (tt0) REVERT: B 229 ASN cc_start: 0.7428 (t0) cc_final: 0.7009 (p0) REVERT: B 242 GLN cc_start: 0.7209 (tp40) cc_final: 0.6973 (tm-30) REVERT: B 323 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7516 (mt-10) REVERT: B 355 LEU cc_start: 0.7836 (tp) cc_final: 0.7580 (tp) REVERT: B 373 GLN cc_start: 0.7608 (mt0) cc_final: 0.7377 (mm110) REVERT: B 386 ASP cc_start: 0.7722 (p0) cc_final: 0.7381 (p0) REVERT: B 402 GLU cc_start: 0.7532 (tp30) cc_final: 0.7264 (tp30) REVERT: B 535 LEU cc_start: 0.7229 (mt) cc_final: 0.6903 (mp) REVERT: B 566 ASN cc_start: 0.8095 (t0) cc_final: 0.7667 (t0) REVERT: B 640 VAL cc_start: 0.8618 (t) cc_final: 0.8350 (m) REVERT: B 656 ARG cc_start: 0.6896 (tpt90) cc_final: 0.6414 (tpt90) REVERT: B 692 MET cc_start: 0.8587 (mtp) cc_final: 0.8342 (mtt) REVERT: B 693 ASP cc_start: 0.8164 (t0) cc_final: 0.7802 (t0) REVERT: B 718 LYS cc_start: 0.8163 (mttm) cc_final: 0.7925 (ttmm) REVERT: A 52 ASP cc_start: 0.8157 (t0) cc_final: 0.7738 (t0) REVERT: A 96 ILE cc_start: 0.6907 (pt) cc_final: 0.6607 (mm) REVERT: A 122 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7628 (tp30) REVERT: A 130 ASP cc_start: 0.8327 (m-30) cc_final: 0.8018 (p0) REVERT: A 162 ASP cc_start: 0.7343 (m-30) cc_final: 0.6791 (t0) REVERT: A 166 MET cc_start: 0.7816 (tpt) cc_final: 0.7584 (tpp) REVERT: A 198 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.7853 (ttm-80) REVERT: A 225 PHE cc_start: 0.7779 (m-80) cc_final: 0.7426 (m-80) REVERT: A 240 LEU cc_start: 0.8064 (tp) cc_final: 0.7734 (tp) REVERT: A 283 LEU cc_start: 0.7896 (mt) cc_final: 0.7661 (mp) REVERT: A 296 ASP cc_start: 0.7792 (t0) cc_final: 0.7486 (t0) REVERT: A 355 LEU cc_start: 0.7303 (tp) cc_final: 0.6766 (tp) REVERT: A 417 VAL cc_start: 0.7812 (t) cc_final: 0.7495 (m) REVERT: A 566 ASN cc_start: 0.8189 (t0) cc_final: 0.7639 (t0) REVERT: A 651 ASP cc_start: 0.8132 (t70) cc_final: 0.7869 (t0) REVERT: A 661 ASP cc_start: 0.7631 (t0) cc_final: 0.7427 (t0) REVERT: A 662 ASP cc_start: 0.6550 (t0) cc_final: 0.6103 (p0) REVERT: A 667 ARG cc_start: 0.7674 (mmm-85) cc_final: 0.7258 (mmm-85) REVERT: A 692 MET cc_start: 0.8278 (mtm) cc_final: 0.8015 (mtp) REVERT: A 713 GLU cc_start: 0.7284 (tt0) cc_final: 0.7076 (tt0) REVERT: A 720 LYS cc_start: 0.7724 (mtpt) cc_final: 0.7509 (mtmm) REVERT: A 759 MET cc_start: 0.8355 (mmm) cc_final: 0.8075 (mmp) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.3294 time to fit residues: 150.7732 Evaluate side-chains 292 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 HIS B 734 GLN B 746 HIS A 49 GLN A 78 ASN A 254 HIS A 264 GLN A 543 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10499 Z= 0.242 Angle : 0.619 7.376 14227 Z= 0.327 Chirality : 0.043 0.188 1630 Planarity : 0.005 0.040 1852 Dihedral : 8.694 166.265 1511 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.40 % Allowed : 13.75 % Favored : 83.86 % 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: 2.07 (0.22), residues: 1301 helix: 2.83 (0.19), residues: 676 sheet: 0.69 (0.37), residues: 185 loop : -0.71 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 137 HIS 0.009 0.002 HIS A 74 PHE 0.017 0.002 PHE A 36 TYR 0.021 0.002 TYR A 31 ARG 0.009 0.001 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 294 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 LEU cc_start: 0.8464 (tp) cc_final: 0.8156 (mm) REVERT: B 205 GLU cc_start: 0.7026 (tt0) cc_final: 0.6763 (tt0) REVERT: B 229 ASN cc_start: 0.7475 (t0) cc_final: 0.6861 (p0) REVERT: B 302 MET cc_start: 0.7242 (ptm) cc_final: 0.6978 (ptt) REVERT: B 323 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7381 (mt-10) REVERT: B 354 ARG cc_start: 0.6788 (mtt180) cc_final: 0.6288 (mtt180) REVERT: B 355 LEU cc_start: 0.7916 (tp) cc_final: 0.7638 (tp) REVERT: B 373 GLN cc_start: 0.7376 (mt0) cc_final: 0.7156 (mm110) REVERT: B 424 VAL cc_start: 0.8325 (t) cc_final: 0.7944 (p) REVERT: B 560 GLU cc_start: 0.7269 (tm-30) cc_final: 0.7061 (tm-30) REVERT: B 566 ASN cc_start: 0.8029 (t0) cc_final: 0.7575 (t0) REVERT: B 624 MET cc_start: 0.8292 (mtp) cc_final: 0.8043 (mtp) REVERT: B 640 VAL cc_start: 0.8513 (t) cc_final: 0.8132 (m) REVERT: B 692 MET cc_start: 0.8374 (mtp) cc_final: 0.8111 (mtt) REVERT: B 693 ASP cc_start: 0.8106 (t0) cc_final: 0.7878 (t70) REVERT: B 723 THR cc_start: 0.8026 (m) cc_final: 0.7707 (p) REVERT: B 739 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6521 (ttm) REVERT: A 36 PHE cc_start: 0.7357 (m-10) cc_final: 0.7152 (m-10) REVERT: A 52 ASP cc_start: 0.8097 (t0) cc_final: 0.7863 (t0) REVERT: A 94 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7109 (mp0) REVERT: A 107 GLU cc_start: 0.7345 (tt0) cc_final: 0.6845 (tm-30) REVERT: A 126 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.7102 (tt0) REVERT: A 157 LEU cc_start: 0.7714 (tt) cc_final: 0.7121 (tp) REVERT: A 198 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.7915 (ttm-80) REVERT: A 240 LEU cc_start: 0.7923 (tp) cc_final: 0.7567 (tp) REVERT: A 242 GLN cc_start: 0.8076 (tp40) cc_final: 0.7822 (tp40) REVERT: A 355 LEU cc_start: 0.7380 (tp) cc_final: 0.6886 (tp) REVERT: A 417 VAL cc_start: 0.7545 (t) cc_final: 0.7303 (p) REVERT: A 565 LEU cc_start: 0.8035 (mt) cc_final: 0.7514 (mt) REVERT: A 566 ASN cc_start: 0.8127 (t0) cc_final: 0.7378 (t0) REVERT: A 590 GLN cc_start: 0.7779 (tp40) cc_final: 0.7578 (tp40) REVERT: A 633 MET cc_start: 0.7765 (mtp) cc_final: 0.7548 (mtm) REVERT: A 651 ASP cc_start: 0.8224 (t70) cc_final: 0.7962 (t0) REVERT: A 662 ASP cc_start: 0.6461 (t0) cc_final: 0.5771 (p0) REVERT: A 667 ARG cc_start: 0.7559 (mmm-85) cc_final: 0.7039 (mmm-85) REVERT: A 692 MET cc_start: 0.8083 (mtm) cc_final: 0.7853 (mtp) REVERT: A 731 GLU cc_start: 0.7541 (mp0) cc_final: 0.7275 (mp0) REVERT: A 751 GLU cc_start: 0.7453 (pm20) cc_final: 0.7095 (pm20) REVERT: A 759 MET cc_start: 0.8282 (mmm) cc_final: 0.8021 (mmp) outliers start: 26 outliers final: 14 residues processed: 306 average time/residue: 0.2902 time to fit residues: 117.2640 Evaluate side-chains 278 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 262 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 695 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 602 ASN B 734 GLN A 74 HIS A 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10499 Z= 0.391 Angle : 0.642 7.787 14227 Z= 0.333 Chirality : 0.045 0.205 1630 Planarity : 0.005 0.089 1852 Dihedral : 7.706 157.629 1511 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.04 % Allowed : 16.33 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.22), residues: 1301 helix: 2.35 (0.19), residues: 667 sheet: 0.62 (0.39), residues: 173 loop : -0.90 (0.25), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 137 HIS 0.008 0.002 HIS A 370 PHE 0.017 0.003 PHE A 30 TYR 0.021 0.002 TYR A 635 ARG 0.006 0.001 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 268 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7732 (ttm170) cc_final: 0.7514 (ttm170) REVERT: B 201 LEU cc_start: 0.8605 (tp) cc_final: 0.7885 (mm) REVERT: B 205 GLU cc_start: 0.7107 (tt0) cc_final: 0.6847 (mp0) REVERT: B 229 ASN cc_start: 0.7546 (t0) cc_final: 0.6868 (p0) REVERT: B 302 MET cc_start: 0.7469 (ptm) cc_final: 0.7213 (ptt) REVERT: B 350 ARG cc_start: 0.6530 (ptt-90) cc_final: 0.6142 (ttp80) REVERT: B 354 ARG cc_start: 0.6818 (mtt180) cc_final: 0.6448 (mtt180) REVERT: B 373 GLN cc_start: 0.7525 (mt0) cc_final: 0.7256 (mm110) REVERT: B 386 ASP cc_start: 0.7711 (p0) cc_final: 0.7346 (p0) REVERT: B 560 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7090 (tm-30) REVERT: B 640 VAL cc_start: 0.8549 (t) cc_final: 0.8185 (m) REVERT: B 662 ASP cc_start: 0.7288 (m-30) cc_final: 0.7032 (p0) REVERT: B 693 ASP cc_start: 0.8112 (t0) cc_final: 0.7900 (t0) REVERT: B 738 LYS cc_start: 0.8236 (mtmm) cc_final: 0.8035 (mtmm) REVERT: B 748 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7231 (m-30) REVERT: B 784 GLU cc_start: 0.7336 (tp30) cc_final: 0.7024 (tp30) REVERT: A 52 ASP cc_start: 0.8189 (t0) cc_final: 0.7667 (t0) REVERT: A 130 ASP cc_start: 0.8334 (m-30) cc_final: 0.8065 (t0) REVERT: A 182 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7570 (pt0) REVERT: A 198 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.7836 (ttm-80) REVERT: A 355 LEU cc_start: 0.7455 (tp) cc_final: 0.7045 (tp) REVERT: A 368 MET cc_start: 0.7550 (ttm) cc_final: 0.7330 (ttm) REVERT: A 417 VAL cc_start: 0.7607 (t) cc_final: 0.7369 (p) REVERT: A 566 ASN cc_start: 0.8119 (t0) cc_final: 0.7387 (t0) REVERT: A 589 GLU cc_start: 0.8049 (tt0) cc_final: 0.7728 (pt0) REVERT: A 662 ASP cc_start: 0.6746 (t0) cc_final: 0.6278 (p0) REVERT: A 667 ARG cc_start: 0.7599 (mmm-85) cc_final: 0.6975 (mmm-85) REVERT: A 751 GLU cc_start: 0.7579 (pm20) cc_final: 0.7168 (pm20) REVERT: A 759 MET cc_start: 0.8228 (mmm) cc_final: 0.7993 (mmp) outliers start: 33 outliers final: 24 residues processed: 281 average time/residue: 0.3107 time to fit residues: 115.9811 Evaluate side-chains 277 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 251 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 723 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 61 optimal weight: 0.0770 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10499 Z= 0.154 Angle : 0.535 10.561 14227 Z= 0.274 Chirality : 0.039 0.141 1630 Planarity : 0.005 0.068 1852 Dihedral : 7.232 160.181 1511 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.58 % Allowed : 17.53 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.23), residues: 1301 helix: 2.71 (0.19), residues: 669 sheet: 0.56 (0.40), residues: 174 loop : -0.88 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 202 HIS 0.005 0.001 HIS A 254 PHE 0.015 0.001 PHE A 334 TYR 0.016 0.001 TYR A 31 ARG 0.006 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 261 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7732 (ttm170) cc_final: 0.7418 (ttm170) REVERT: B 156 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7844 (mtt90) REVERT: B 201 LEU cc_start: 0.8555 (tp) cc_final: 0.7603 (mm) REVERT: B 205 GLU cc_start: 0.6958 (tt0) cc_final: 0.6696 (mp0) REVERT: B 229 ASN cc_start: 0.7458 (t0) cc_final: 0.6762 (p0) REVERT: B 302 MET cc_start: 0.7121 (ptm) cc_final: 0.6833 (ptt) REVERT: B 350 ARG cc_start: 0.6543 (ptt-90) cc_final: 0.6106 (ttp80) REVERT: B 373 GLN cc_start: 0.7497 (mt0) cc_final: 0.7244 (mm110) REVERT: B 560 GLU cc_start: 0.7273 (tm-30) cc_final: 0.7002 (tm-30) REVERT: B 566 ASN cc_start: 0.7980 (t0) cc_final: 0.7562 (t0) REVERT: B 609 MET cc_start: 0.7683 (ttt) cc_final: 0.7440 (ttt) REVERT: B 640 VAL cc_start: 0.8549 (t) cc_final: 0.8149 (m) REVERT: B 662 ASP cc_start: 0.7300 (m-30) cc_final: 0.7048 (p0) REVERT: B 695 ILE cc_start: 0.7820 (tt) cc_final: 0.7610 (mm) REVERT: B 723 THR cc_start: 0.7982 (m) cc_final: 0.7637 (p) REVERT: B 750 LEU cc_start: 0.8149 (tp) cc_final: 0.7357 (pp) REVERT: B 784 GLU cc_start: 0.7122 (tp30) cc_final: 0.6821 (tp30) REVERT: A 33 MET cc_start: 0.7655 (mmm) cc_final: 0.7401 (mmt) REVERT: A 52 ASP cc_start: 0.8083 (t0) cc_final: 0.7335 (t0) REVERT: A 107 GLU cc_start: 0.7818 (tt0) cc_final: 0.7187 (tm-30) REVERT: A 198 ARG cc_start: 0.8402 (ttm-80) cc_final: 0.7831 (ttm-80) REVERT: A 355 LEU cc_start: 0.7231 (tp) cc_final: 0.6829 (tp) REVERT: A 417 VAL cc_start: 0.7605 (t) cc_final: 0.7371 (p) REVERT: A 566 ASN cc_start: 0.8133 (t0) cc_final: 0.7411 (t0) REVERT: A 589 GLU cc_start: 0.8002 (tt0) cc_final: 0.7757 (pt0) REVERT: A 662 ASP cc_start: 0.6432 (t0) cc_final: 0.5913 (p0) REVERT: A 667 ARG cc_start: 0.7467 (mmm-85) cc_final: 0.6707 (mmm-85) REVERT: A 751 GLU cc_start: 0.7333 (pm20) cc_final: 0.6957 (pm20) REVERT: A 759 MET cc_start: 0.8079 (mmm) cc_final: 0.7869 (mmp) outliers start: 28 outliers final: 13 residues processed: 273 average time/residue: 0.3143 time to fit residues: 111.4024 Evaluate side-chains 262 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 249 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 695 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS A 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10499 Z= 0.278 Angle : 0.577 10.273 14227 Z= 0.294 Chirality : 0.041 0.140 1630 Planarity : 0.005 0.076 1852 Dihedral : 7.234 158.484 1511 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.00 % Favored : 97.92 % Rotamer: Outliers : 3.23 % Allowed : 17.62 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.23), residues: 1301 helix: 2.54 (0.19), residues: 667 sheet: 0.40 (0.40), residues: 171 loop : -0.95 (0.25), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 137 HIS 0.007 0.001 HIS A 254 PHE 0.012 0.002 PHE A 725 TYR 0.017 0.002 TYR A 635 ARG 0.007 0.001 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 260 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7776 (ttm170) cc_final: 0.7428 (ttm170) REVERT: B 197 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7828 (mtp180) REVERT: B 198 ARG cc_start: 0.8316 (mtm110) cc_final: 0.8011 (mmm-85) REVERT: B 201 LEU cc_start: 0.8624 (tp) cc_final: 0.8041 (tp) REVERT: B 229 ASN cc_start: 0.7636 (t0) cc_final: 0.6865 (p0) REVERT: B 302 MET cc_start: 0.7402 (ptm) cc_final: 0.7128 (ptt) REVERT: B 334 PHE cc_start: 0.7058 (m-10) cc_final: 0.6689 (m-80) REVERT: B 350 ARG cc_start: 0.6654 (ptt-90) cc_final: 0.5832 (ttp80) REVERT: B 354 ARG cc_start: 0.6822 (mtt180) cc_final: 0.6325 (mtt180) REVERT: B 373 GLN cc_start: 0.7523 (mt0) cc_final: 0.7258 (mm110) REVERT: B 560 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7141 (tm-30) REVERT: B 640 VAL cc_start: 0.8567 (t) cc_final: 0.8235 (m) REVERT: B 662 ASP cc_start: 0.7293 (m-30) cc_final: 0.7044 (p0) REVERT: B 723 THR cc_start: 0.7921 (m) cc_final: 0.7560 (p) REVERT: B 750 LEU cc_start: 0.8209 (tp) cc_final: 0.7453 (pp) REVERT: B 784 GLU cc_start: 0.7262 (tp30) cc_final: 0.6926 (tp30) REVERT: A 52 ASP cc_start: 0.8177 (t0) cc_final: 0.7399 (t0) REVERT: A 107 GLU cc_start: 0.8001 (tt0) cc_final: 0.7363 (tm-30) REVERT: A 186 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7449 (mt-10) REVERT: A 198 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.7680 (ttm-80) REVERT: A 355 LEU cc_start: 0.7282 (tp) cc_final: 0.6927 (tp) REVERT: A 417 VAL cc_start: 0.7629 (t) cc_final: 0.7415 (p) REVERT: A 566 ASN cc_start: 0.8122 (t0) cc_final: 0.7404 (t0) REVERT: A 589 GLU cc_start: 0.8008 (tt0) cc_final: 0.7767 (pt0) REVERT: A 662 ASP cc_start: 0.6679 (t0) cc_final: 0.6125 (p0) REVERT: A 667 ARG cc_start: 0.7496 (mmm-85) cc_final: 0.6744 (mmm-85) REVERT: A 751 GLU cc_start: 0.7379 (pm20) cc_final: 0.7049 (pm20) outliers start: 35 outliers final: 27 residues processed: 276 average time/residue: 0.3014 time to fit residues: 108.8139 Evaluate side-chains 280 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 253 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS A 344 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10499 Z= 0.227 Angle : 0.553 7.712 14227 Z= 0.284 Chirality : 0.039 0.137 1630 Planarity : 0.005 0.067 1852 Dihedral : 7.139 158.402 1511 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.69 % Favored : 98.23 % Rotamer: Outliers : 2.68 % Allowed : 19.19 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.23), residues: 1301 helix: 2.59 (0.19), residues: 661 sheet: 0.17 (0.38), residues: 187 loop : -0.94 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 137 HIS 0.006 0.001 HIS A 254 PHE 0.010 0.001 PHE A 143 TYR 0.016 0.001 TYR A 31 ARG 0.007 0.000 ARG A 794 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 261 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7786 (ttm170) cc_final: 0.7428 (ttm170) REVERT: B 202 TRP cc_start: 0.8059 (p-90) cc_final: 0.7828 (p-90) REVERT: B 205 GLU cc_start: 0.6854 (mp0) cc_final: 0.6448 (mp0) REVERT: B 229 ASN cc_start: 0.7666 (t0) cc_final: 0.6875 (p0) REVERT: B 302 MET cc_start: 0.7335 (ptm) cc_final: 0.7051 (ptt) REVERT: B 334 PHE cc_start: 0.7016 (m-10) cc_final: 0.6662 (m-80) REVERT: B 350 ARG cc_start: 0.6662 (ptt-90) cc_final: 0.5856 (ttp80) REVERT: B 354 ARG cc_start: 0.6840 (mtt180) cc_final: 0.6389 (mtt180) REVERT: B 373 GLN cc_start: 0.7517 (mt0) cc_final: 0.7232 (mm110) REVERT: B 560 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7181 (tm-30) REVERT: B 640 VAL cc_start: 0.8546 (t) cc_final: 0.8207 (m) REVERT: B 662 ASP cc_start: 0.7293 (m-30) cc_final: 0.7054 (p0) REVERT: B 750 LEU cc_start: 0.8203 (tp) cc_final: 0.7455 (pp) REVERT: B 784 GLU cc_start: 0.7226 (tp30) cc_final: 0.6941 (tp30) REVERT: A 52 ASP cc_start: 0.8052 (t0) cc_final: 0.7286 (t0) REVERT: A 107 GLU cc_start: 0.8013 (tt0) cc_final: 0.7382 (tm-30) REVERT: A 166 MET cc_start: 0.7632 (tpp) cc_final: 0.7419 (tpp) REVERT: A 198 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.7651 (ttm-80) REVERT: A 355 LEU cc_start: 0.7236 (tp) cc_final: 0.6914 (tp) REVERT: A 417 VAL cc_start: 0.7652 (t) cc_final: 0.7434 (p) REVERT: A 566 ASN cc_start: 0.8094 (t0) cc_final: 0.7418 (t0) REVERT: A 589 GLU cc_start: 0.7995 (tt0) cc_final: 0.7787 (pt0) REVERT: A 662 ASP cc_start: 0.6667 (t0) cc_final: 0.6160 (p0) REVERT: A 667 ARG cc_start: 0.7470 (mmm-85) cc_final: 0.6727 (mmm-85) REVERT: A 751 GLU cc_start: 0.7359 (pm20) cc_final: 0.7066 (pm20) outliers start: 29 outliers final: 25 residues processed: 277 average time/residue: 0.2829 time to fit residues: 103.0647 Evaluate side-chains 275 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 250 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 58 optimal weight: 0.0980 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10499 Z= 0.340 Angle : 0.603 7.635 14227 Z= 0.309 Chirality : 0.042 0.153 1630 Planarity : 0.005 0.064 1852 Dihedral : 7.227 157.122 1511 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.00 % Favored : 97.92 % Rotamer: Outliers : 3.04 % Allowed : 19.00 % Favored : 77.95 % 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: 1.32 (0.23), residues: 1301 helix: 2.32 (0.19), residues: 661 sheet: 0.17 (0.38), residues: 185 loop : -1.03 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 137 HIS 0.006 0.002 HIS A 585 PHE 0.030 0.002 PHE A 36 TYR 0.018 0.002 TYR A 635 ARG 0.007 0.001 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 261 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7771 (ttm170) cc_final: 0.7427 (ttm170) REVERT: B 166 MET cc_start: 0.7885 (tpp) cc_final: 0.7463 (tpp) REVERT: B 197 ARG cc_start: 0.8190 (mtp180) cc_final: 0.7988 (mtp180) REVERT: B 201 LEU cc_start: 0.8338 (tp) cc_final: 0.8093 (tt) REVERT: B 202 TRP cc_start: 0.8072 (p-90) cc_final: 0.7814 (p-90) REVERT: B 205 GLU cc_start: 0.6960 (mp0) cc_final: 0.6506 (mp0) REVERT: B 229 ASN cc_start: 0.7692 (t0) cc_final: 0.6990 (p0) REVERT: B 302 MET cc_start: 0.7331 (ptm) cc_final: 0.7063 (ptt) REVERT: B 334 PHE cc_start: 0.7070 (m-10) cc_final: 0.6709 (m-80) REVERT: B 350 ARG cc_start: 0.6664 (ptt-90) cc_final: 0.6151 (ttp80) REVERT: B 373 GLN cc_start: 0.7518 (mt0) cc_final: 0.7237 (mm110) REVERT: B 393 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6363 (mp) REVERT: B 560 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7208 (tm-30) REVERT: B 635 TYR cc_start: 0.8271 (m-80) cc_final: 0.7972 (m-80) REVERT: B 640 VAL cc_start: 0.8530 (t) cc_final: 0.8190 (m) REVERT: B 662 ASP cc_start: 0.7287 (m-30) cc_final: 0.7025 (p0) REVERT: B 750 LEU cc_start: 0.8232 (tp) cc_final: 0.7587 (pp) REVERT: B 784 GLU cc_start: 0.7343 (tp30) cc_final: 0.7002 (tp30) REVERT: A 52 ASP cc_start: 0.8158 (t0) cc_final: 0.7376 (t0) REVERT: A 107 GLU cc_start: 0.8164 (tt0) cc_final: 0.7553 (tm-30) REVERT: A 166 MET cc_start: 0.7636 (tpp) cc_final: 0.7355 (tpp) REVERT: A 186 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7467 (mp0) REVERT: A 198 ARG cc_start: 0.8370 (ttm-80) cc_final: 0.7922 (ttm-80) REVERT: A 355 LEU cc_start: 0.7317 (tp) cc_final: 0.6989 (tp) REVERT: A 566 ASN cc_start: 0.8086 (t0) cc_final: 0.7404 (t0) REVERT: A 589 GLU cc_start: 0.8006 (tt0) cc_final: 0.7777 (pt0) REVERT: A 662 ASP cc_start: 0.6739 (t0) cc_final: 0.6242 (p0) REVERT: A 667 ARG cc_start: 0.7479 (mmm-85) cc_final: 0.6746 (mmm-85) REVERT: A 794 ARG cc_start: 0.7590 (ttm-80) cc_final: 0.7342 (mtm110) outliers start: 33 outliers final: 26 residues processed: 281 average time/residue: 0.2864 time to fit residues: 104.8524 Evaluate side-chains 283 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 256 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.4980 chunk 50 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10499 Z= 0.160 Angle : 0.534 7.740 14227 Z= 0.273 Chirality : 0.038 0.131 1630 Planarity : 0.004 0.052 1852 Dihedral : 7.031 158.443 1511 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.69 % Favored : 98.23 % Rotamer: Outliers : 2.40 % Allowed : 19.83 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.23), residues: 1301 helix: 2.69 (0.20), residues: 664 sheet: 0.03 (0.36), residues: 209 loop : -0.88 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 202 HIS 0.006 0.001 HIS A 254 PHE 0.020 0.001 PHE A 36 TYR 0.015 0.001 TYR A 31 ARG 0.008 0.000 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 266 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7755 (ttm170) cc_final: 0.7404 (ttm170) REVERT: B 197 ARG cc_start: 0.8337 (mtp180) cc_final: 0.8133 (mtp180) REVERT: B 201 LEU cc_start: 0.8372 (tp) cc_final: 0.8113 (tt) REVERT: B 205 GLU cc_start: 0.6959 (mp0) cc_final: 0.6466 (mp0) REVERT: B 302 MET cc_start: 0.7135 (ptm) cc_final: 0.6840 (ptt) REVERT: B 334 PHE cc_start: 0.7112 (m-10) cc_final: 0.6775 (m-80) REVERT: B 350 ARG cc_start: 0.6626 (ptt-90) cc_final: 0.6144 (ttp-110) REVERT: B 354 ARG cc_start: 0.6799 (mtt180) cc_final: 0.6427 (mtt180) REVERT: B 373 GLN cc_start: 0.7506 (mt0) cc_final: 0.7223 (mm110) REVERT: B 560 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7120 (tm-30) REVERT: B 566 ASN cc_start: 0.7974 (t0) cc_final: 0.7560 (t0) REVERT: B 609 MET cc_start: 0.7782 (ttt) cc_final: 0.7567 (ttt) REVERT: B 640 VAL cc_start: 0.8403 (t) cc_final: 0.8107 (m) REVERT: B 656 ARG cc_start: 0.6903 (tpt90) cc_final: 0.6315 (tpt90) REVERT: B 662 ASP cc_start: 0.7298 (m-30) cc_final: 0.7038 (p0) REVERT: B 723 THR cc_start: 0.7777 (m) cc_final: 0.7552 (p) REVERT: B 738 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7892 (mtmm) REVERT: B 750 LEU cc_start: 0.8214 (tp) cc_final: 0.7477 (pp) REVERT: B 784 GLU cc_start: 0.7196 (tp30) cc_final: 0.6898 (tp30) REVERT: A 33 MET cc_start: 0.7627 (mmm) cc_final: 0.7330 (mmt) REVERT: A 52 ASP cc_start: 0.7932 (t0) cc_final: 0.7244 (t0) REVERT: A 107 GLU cc_start: 0.7962 (tt0) cc_final: 0.7350 (tm-30) REVERT: A 166 MET cc_start: 0.7639 (tpp) cc_final: 0.7318 (tpp) REVERT: A 198 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.7885 (ttm-80) REVERT: A 219 THR cc_start: 0.7817 (m) cc_final: 0.7370 (p) REVERT: A 355 LEU cc_start: 0.7176 (tp) cc_final: 0.6843 (tp) REVERT: A 566 ASN cc_start: 0.8064 (t0) cc_final: 0.7409 (t0) REVERT: A 662 ASP cc_start: 0.6587 (t0) cc_final: 0.6078 (p0) REVERT: A 667 ARG cc_start: 0.7375 (mmm-85) cc_final: 0.6626 (mmm-85) REVERT: A 751 GLU cc_start: 0.7459 (pm20) cc_final: 0.7124 (pm20) REVERT: A 794 ARG cc_start: 0.7551 (ttm-80) cc_final: 0.7303 (mtm110) outliers start: 26 outliers final: 19 residues processed: 278 average time/residue: 0.2949 time to fit residues: 107.0808 Evaluate side-chains 282 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 263 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 117 optimal weight: 0.0030 chunk 70 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 0.3980 chunk 36 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 overall best weight: 2.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 744 ASN A 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10499 Z= 0.224 Angle : 0.567 8.264 14227 Z= 0.290 Chirality : 0.039 0.134 1630 Planarity : 0.004 0.041 1852 Dihedral : 7.051 157.088 1511 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.84 % Favored : 98.08 % Rotamer: Outliers : 2.21 % Allowed : 20.57 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.23), residues: 1301 helix: 2.57 (0.20), residues: 664 sheet: 0.20 (0.39), residues: 186 loop : -0.91 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 137 HIS 0.008 0.001 HIS A 254 PHE 0.018 0.002 PHE A 334 TYR 0.016 0.001 TYR A 31 ARG 0.008 0.000 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 264 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7776 (ttm170) cc_final: 0.7422 (ttm170) REVERT: B 197 ARG cc_start: 0.8330 (mtp180) cc_final: 0.8114 (mtp180) REVERT: B 201 LEU cc_start: 0.8343 (tp) cc_final: 0.7939 (tt) REVERT: B 205 GLU cc_start: 0.7086 (mp0) cc_final: 0.6451 (mp0) REVERT: B 229 ASN cc_start: 0.7974 (m-40) cc_final: 0.6699 (p0) REVERT: B 302 MET cc_start: 0.7264 (ptm) cc_final: 0.6977 (ptt) REVERT: B 350 ARG cc_start: 0.6658 (ptt-90) cc_final: 0.6148 (ttp80) REVERT: B 354 ARG cc_start: 0.6802 (mtt180) cc_final: 0.6514 (mtt180) REVERT: B 373 GLN cc_start: 0.7520 (mt0) cc_final: 0.7232 (mm110) REVERT: B 560 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7185 (tm-30) REVERT: B 566 ASN cc_start: 0.7995 (t0) cc_final: 0.7585 (t0) REVERT: B 579 ARG cc_start: 0.8370 (ttm110) cc_final: 0.7959 (ttm110) REVERT: B 640 VAL cc_start: 0.8379 (t) cc_final: 0.8103 (m) REVERT: B 662 ASP cc_start: 0.7285 (m-30) cc_final: 0.7015 (p0) REVERT: B 697 ARG cc_start: 0.7245 (mmp-170) cc_final: 0.6337 (mmm160) REVERT: B 738 LYS cc_start: 0.8249 (mtmm) cc_final: 0.7911 (mtmm) REVERT: B 750 LEU cc_start: 0.8222 (tp) cc_final: 0.7518 (pp) REVERT: B 784 GLU cc_start: 0.7246 (tp30) cc_final: 0.6950 (tp30) REVERT: A 33 MET cc_start: 0.7631 (mmm) cc_final: 0.7330 (mmt) REVERT: A 52 ASP cc_start: 0.8029 (t0) cc_final: 0.7330 (t0) REVERT: A 107 GLU cc_start: 0.8002 (tt0) cc_final: 0.7391 (tm-30) REVERT: A 166 MET cc_start: 0.7643 (tpp) cc_final: 0.7272 (tpp) REVERT: A 198 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.7891 (ttm-80) REVERT: A 219 THR cc_start: 0.7858 (m) cc_final: 0.7405 (p) REVERT: A 355 LEU cc_start: 0.7214 (tp) cc_final: 0.6903 (tp) REVERT: A 566 ASN cc_start: 0.8036 (t0) cc_final: 0.7363 (t0) REVERT: A 751 GLU cc_start: 0.7385 (pm20) cc_final: 0.6961 (pm20) REVERT: A 794 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.7324 (mtm110) outliers start: 24 outliers final: 23 residues processed: 278 average time/residue: 0.2912 time to fit residues: 105.3037 Evaluate side-chains 288 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 265 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 744 ASN A 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10499 Z= 0.354 Angle : 0.645 9.514 14227 Z= 0.328 Chirality : 0.042 0.165 1630 Planarity : 0.005 0.047 1852 Dihedral : 7.212 156.110 1511 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.15 % Favored : 97.77 % Rotamer: Outliers : 2.40 % Allowed : 20.57 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.23), residues: 1301 helix: 2.26 (0.20), residues: 663 sheet: 0.17 (0.39), residues: 184 loop : -1.00 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 137 HIS 0.008 0.002 HIS A 254 PHE 0.016 0.002 PHE A 204 TYR 0.020 0.002 TYR B 635 ARG 0.008 0.001 ARG B 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 260 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7801 (ttm170) cc_final: 0.7446 (ttm170) REVERT: B 197 ARG cc_start: 0.8268 (mtp180) cc_final: 0.8041 (mtp180) REVERT: B 201 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8083 (tt) REVERT: B 205 GLU cc_start: 0.7152 (mp0) cc_final: 0.6669 (mp0) REVERT: B 229 ASN cc_start: 0.7976 (m-40) cc_final: 0.6681 (p0) REVERT: B 302 MET cc_start: 0.7359 (ptm) cc_final: 0.7101 (ptt) REVERT: B 350 ARG cc_start: 0.6646 (ptt-90) cc_final: 0.6042 (ttp80) REVERT: B 354 ARG cc_start: 0.6738 (mtt180) cc_final: 0.6190 (mtt180) REVERT: B 373 GLN cc_start: 0.7540 (mt0) cc_final: 0.7254 (mm110) REVERT: B 393 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6331 (mp) REVERT: B 560 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7232 (tm-30) REVERT: B 579 ARG cc_start: 0.8357 (ttm110) cc_final: 0.7920 (ttm110) REVERT: B 635 TYR cc_start: 0.8277 (m-80) cc_final: 0.7961 (m-80) REVERT: B 640 VAL cc_start: 0.8398 (t) cc_final: 0.8162 (m) REVERT: B 656 ARG cc_start: 0.6953 (tpt90) cc_final: 0.6304 (tpt90) REVERT: B 662 ASP cc_start: 0.7276 (m-30) cc_final: 0.6938 (p0) REVERT: B 693 ASP cc_start: 0.8050 (t0) cc_final: 0.7597 (t0) REVERT: B 734 GLN cc_start: 0.8017 (mt0) cc_final: 0.7803 (mt0) REVERT: B 738 LYS cc_start: 0.8246 (mtmm) cc_final: 0.7860 (mtmm) REVERT: B 750 LEU cc_start: 0.8283 (tp) cc_final: 0.7661 (pp) REVERT: B 784 GLU cc_start: 0.7389 (tp30) cc_final: 0.7029 (tp30) REVERT: A 52 ASP cc_start: 0.8098 (t0) cc_final: 0.7354 (t0) REVERT: A 107 GLU cc_start: 0.8271 (tt0) cc_final: 0.7699 (tm-30) REVERT: A 166 MET cc_start: 0.7727 (tpp) cc_final: 0.7343 (tpp) REVERT: A 186 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7425 (mp0) REVERT: A 198 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.7882 (ttm-80) REVERT: A 275 ARG cc_start: 0.7699 (mtp180) cc_final: 0.7456 (mtp180) REVERT: A 355 LEU cc_start: 0.7367 (tp) cc_final: 0.7050 (tp) REVERT: A 566 ASN cc_start: 0.7999 (t0) cc_final: 0.7323 (t0) REVERT: A 662 ASP cc_start: 0.6987 (m-30) cc_final: 0.6272 (t70) REVERT: A 751 GLU cc_start: 0.7431 (pm20) cc_final: 0.7000 (pm20) REVERT: A 794 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.7361 (mtm110) outliers start: 26 outliers final: 23 residues processed: 273 average time/residue: 0.2810 time to fit residues: 100.8874 Evaluate side-chains 280 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 255 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 544 GLN B 744 ASN A 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112424 restraints weight = 19350.020| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.38 r_work: 0.3255 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10499 Z= 0.201 Angle : 0.575 8.725 14227 Z= 0.293 Chirality : 0.039 0.137 1630 Planarity : 0.004 0.042 1852 Dihedral : 7.110 157.148 1511 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.92 % Favored : 98.00 % Rotamer: Outliers : 1.85 % Allowed : 21.03 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.23), residues: 1301 helix: 2.48 (0.20), residues: 660 sheet: 0.18 (0.39), residues: 184 loop : -0.91 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 137 HIS 0.008 0.001 HIS A 254 PHE 0.012 0.001 PHE B 143 TYR 0.016 0.001 TYR A 31 ARG 0.009 0.000 ARG B 220 =============================================================================== Job complete usr+sys time: 2672.11 seconds wall clock time: 48 minutes 2.02 seconds (2882.02 seconds total)