Starting phenix.real_space_refine on Sat Jul 20 09:42:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/07_2024/7oto_13063_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/07_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_13063/07_2024/7oto_13063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/07_2024/7oto_13063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/07_2024/7oto_13063_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/07_2024/7oto_13063_neut.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 Residue "B GLU 186": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B ARG 656": "NH1" <-> "NH2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 694": "OE1" <-> "OE2" Residue "B ARG 697": "NH1" <-> "NH2" Residue "B GLU 751": "OE1" <-> "OE2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A ARG 108": "NH1" <-> "NH2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A GLU 540": "OE1" <-> "OE2" Residue "A GLU 646": "OE1" <-> "OE2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A ARG 697": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.75, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 4.22 Conformation dependent library (CDL) restraints added in 2.0 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: 1.21 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: 3.31 Time building geometry restraints manager: 4.59 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: 99.02 - 106.08: 348 106.08 - 113.14: 5052 113.14 - 120.20: 5078 120.20 - 127.26: 3683 127.26 - 134.32: 66 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 ========== 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: 0.090 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 30.760 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: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.090 ------------------------------------------------------------------------------- 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 : 1.171 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: 0.3303 time to fit residues: 151.8693 Evaluate side-chains 292 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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: 8.9990 chunk 99 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 GLN 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10499 Z= 0.192 Angle : 0.585 7.559 14227 Z= 0.306 Chirality : 0.041 0.179 1630 Planarity : 0.005 0.040 1852 Dihedral : 8.396 164.672 1511 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.77 % Allowed : 13.65 % Favored : 83.58 % 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: 2.09 (0.22), residues: 1301 helix: 2.86 (0.19), residues: 679 sheet: 0.61 (0.36), residues: 196 loop : -0.75 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 137 HIS 0.009 0.001 HIS A 74 PHE 0.014 0.002 PHE A 36 TYR 0.019 0.002 TYR A 31 ARG 0.010 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 319 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 289 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7732 (ttm170) cc_final: 0.7521 (ttm170) REVERT: B 201 LEU cc_start: 0.8453 (tp) cc_final: 0.8090 (mm) REVERT: B 205 GLU cc_start: 0.6971 (tt0) cc_final: 0.6646 (tt0) REVERT: B 229 ASN cc_start: 0.7409 (t0) cc_final: 0.6784 (p0) REVERT: B 302 MET cc_start: 0.7092 (ptm) cc_final: 0.6844 (ptt) REVERT: B 355 LEU cc_start: 0.7893 (tp) cc_final: 0.7624 (tp) REVERT: B 373 GLN cc_start: 0.7368 (mt0) cc_final: 0.7162 (mm110) REVERT: B 424 VAL cc_start: 0.8192 (t) cc_final: 0.7782 (p) REVERT: B 560 GLU cc_start: 0.7221 (tm-30) cc_final: 0.7000 (tm-30) REVERT: B 566 ASN cc_start: 0.7999 (t0) cc_final: 0.7593 (t0) REVERT: B 609 MET cc_start: 0.7471 (ttt) cc_final: 0.7201 (ttt) REVERT: B 624 MET cc_start: 0.8272 (mtp) cc_final: 0.7998 (mtp) REVERT: B 640 VAL cc_start: 0.8475 (t) cc_final: 0.8075 (m) REVERT: B 692 MET cc_start: 0.8344 (mtp) cc_final: 0.8067 (mtt) REVERT: B 693 ASP cc_start: 0.8120 (t0) cc_final: 0.7900 (t70) REVERT: B 723 THR cc_start: 0.7988 (m) cc_final: 0.7699 (p) REVERT: B 739 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6460 (ttm) REVERT: A 33 MET cc_start: 0.7680 (mmm) cc_final: 0.7476 (mmt) REVERT: A 52 ASP cc_start: 0.7953 (t0) cc_final: 0.7032 (t0) REVERT: A 107 GLU cc_start: 0.7270 (tt0) cc_final: 0.6761 (tm-30) REVERT: A 126 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.7035 (tt0) REVERT: A 130 ASP cc_start: 0.8275 (m-30) cc_final: 0.7924 (t0) REVERT: A 133 LEU cc_start: 0.8225 (tp) cc_final: 0.8024 (tp) REVERT: A 149 ASP cc_start: 0.7431 (t0) cc_final: 0.7118 (t0) REVERT: A 157 LEU cc_start: 0.7619 (tt) cc_final: 0.7082 (tp) REVERT: A 198 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.7946 (ttm-80) REVERT: A 225 PHE cc_start: 0.7877 (m-80) cc_final: 0.7515 (m-80) REVERT: A 240 LEU cc_start: 0.7925 (tp) cc_final: 0.7543 (tp) REVERT: A 242 GLN cc_start: 0.8065 (tp40) cc_final: 0.7823 (tp40) REVERT: A 296 ASP cc_start: 0.7818 (t0) cc_final: 0.7447 (t0) REVERT: A 355 LEU cc_start: 0.7368 (tp) cc_final: 0.6884 (tp) REVERT: A 417 VAL cc_start: 0.7543 (t) cc_final: 0.7299 (p) REVERT: A 565 LEU cc_start: 0.8035 (mt) cc_final: 0.7535 (mt) REVERT: A 566 ASN cc_start: 0.8090 (t0) cc_final: 0.7401 (t0) REVERT: A 590 GLN cc_start: 0.7726 (tp40) cc_final: 0.7516 (tp40) REVERT: A 633 MET cc_start: 0.7580 (mtp) cc_final: 0.7341 (mtm) REVERT: A 651 ASP cc_start: 0.8227 (t70) cc_final: 0.7978 (t0) REVERT: A 662 ASP cc_start: 0.6469 (t0) cc_final: 0.5924 (t0) REVERT: A 692 MET cc_start: 0.8049 (mtm) cc_final: 0.7807 (mtp) REVERT: A 720 LYS cc_start: 0.7744 (mtpt) cc_final: 0.7519 (mtmm) REVERT: A 731 GLU cc_start: 0.7542 (mp0) cc_final: 0.7255 (mp0) REVERT: A 759 MET cc_start: 0.8335 (mmm) cc_final: 0.8095 (mmp) REVERT: A 778 LEU cc_start: 0.7847 (tp) cc_final: 0.7565 (tt) outliers start: 30 outliers final: 17 residues processed: 304 average time/residue: 0.2939 time to fit residues: 117.1913 Evaluate side-chains 286 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 267 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 348 LEU Chi-restraints excluded: chain B residue 531 LEU 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 150 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 657 VAL 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: 0.7980 chunk 36 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 119 optimal weight: 0.2980 chunk 128 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN B 602 ASN A 74 HIS A 254 HIS A 616 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10499 Z= 0.306 Angle : 0.582 6.521 14227 Z= 0.303 Chirality : 0.042 0.178 1630 Planarity : 0.005 0.038 1852 Dihedral : 7.535 156.101 1511 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.41 % Allowed : 16.33 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.22), residues: 1301 helix: 2.64 (0.19), residues: 666 sheet: 0.56 (0.36), residues: 196 loop : -0.90 (0.25), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 137 HIS 0.007 0.002 HIS A 370 PHE 0.030 0.002 PHE A 36 TYR 0.018 0.002 TYR A 635 ARG 0.007 0.001 ARG B 667 *********************** 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 307 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 270 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 201 LEU cc_start: 0.8578 (tp) cc_final: 0.7607 (mm) REVERT: B 205 GLU cc_start: 0.7059 (tt0) cc_final: 0.6763 (mp0) REVERT: B 229 ASN cc_start: 0.7483 (t0) cc_final: 0.6801 (p0) REVERT: B 242 GLN cc_start: 0.7046 (mm-40) cc_final: 0.6534 (tm-30) REVERT: B 302 MET cc_start: 0.7338 (ptm) cc_final: 0.7036 (ptt) REVERT: B 373 GLN cc_start: 0.7499 (mt0) cc_final: 0.7254 (mm110) REVERT: B 560 GLU cc_start: 0.7326 (tm-30) cc_final: 0.7043 (tm-30) REVERT: B 624 MET cc_start: 0.8237 (mtp) cc_final: 0.8026 (mtp) REVERT: B 693 ASP cc_start: 0.8130 (t0) cc_final: 0.7878 (t0) REVERT: B 723 THR cc_start: 0.7959 (m) cc_final: 0.7588 (p) REVERT: B 738 LYS cc_start: 0.8264 (mtmm) cc_final: 0.7861 (mtmm) REVERT: B 784 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6941 (tp30) REVERT: A 33 MET cc_start: 0.7624 (mmm) cc_final: 0.7388 (mmt) REVERT: A 107 GLU cc_start: 0.7786 (tt0) cc_final: 0.7156 (tm-30) REVERT: A 126 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: A 130 ASP cc_start: 0.8300 (m-30) cc_final: 0.7850 (t0) REVERT: A 149 ASP cc_start: 0.7493 (t0) cc_final: 0.7187 (t0) REVERT: A 182 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7644 (pt0) REVERT: A 198 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.7875 (ttm-80) REVERT: A 355 LEU cc_start: 0.7427 (tp) cc_final: 0.7031 (tp) REVERT: A 417 VAL cc_start: 0.7592 (t) cc_final: 0.7359 (p) REVERT: A 566 ASN cc_start: 0.8067 (t0) cc_final: 0.7365 (t0) REVERT: A 571 THR cc_start: 0.8417 (p) cc_final: 0.8212 (p) REVERT: A 651 ASP cc_start: 0.8207 (t70) cc_final: 0.7993 (t0) REVERT: A 662 ASP cc_start: 0.6507 (t0) cc_final: 0.6030 (t70) REVERT: A 692 MET cc_start: 0.8100 (mtm) cc_final: 0.7896 (mtp) REVERT: A 720 LYS cc_start: 0.7739 (mtpt) cc_final: 0.7501 (mtmm) REVERT: A 751 GLU cc_start: 0.7301 (pm20) cc_final: 0.7031 (pm20) REVERT: A 759 MET cc_start: 0.8238 (mmm) cc_final: 0.7999 (mmp) outliers start: 37 outliers final: 23 residues processed: 285 average time/residue: 0.3128 time to fit residues: 117.1372 Evaluate side-chains 277 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 251 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 322 LEU 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 645 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 126 GLN 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 574 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 13 optimal weight: 0.0070 chunk 56 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10499 Z= 0.277 Angle : 0.567 10.131 14227 Z= 0.290 Chirality : 0.041 0.149 1630 Planarity : 0.005 0.039 1852 Dihedral : 7.285 155.586 1511 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.00 % Favored : 97.92 % Rotamer: Outliers : 3.87 % Allowed : 17.25 % Favored : 78.87 % 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: 1.64 (0.22), residues: 1301 helix: 2.51 (0.19), residues: 666 sheet: 0.57 (0.38), residues: 184 loop : -0.93 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 137 HIS 0.005 0.002 HIS A 74 PHE 0.024 0.002 PHE A 36 TYR 0.017 0.002 TYR A 635 ARG 0.006 0.001 ARG B 220 *********************** 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 302 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 260 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: B 156 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7839 (mtt180) REVERT: B 201 LEU cc_start: 0.8600 (tp) cc_final: 0.7657 (mm) REVERT: B 205 GLU cc_start: 0.7036 (tt0) cc_final: 0.6778 (mp0) REVERT: B 229 ASN cc_start: 0.7562 (t0) cc_final: 0.6861 (p0) REVERT: B 242 GLN cc_start: 0.7064 (mm-40) cc_final: 0.6542 (tm-30) REVERT: B 302 MET cc_start: 0.7320 (ptm) cc_final: 0.7022 (ptt) REVERT: B 373 GLN cc_start: 0.7490 (mt0) cc_final: 0.7222 (mm110) REVERT: B 560 GLU cc_start: 0.7321 (tm-30) cc_final: 0.7005 (tm-30) REVERT: B 640 VAL cc_start: 0.8533 (t) cc_final: 0.8121 (m) REVERT: B 693 ASP cc_start: 0.8107 (t0) cc_final: 0.7855 (t70) REVERT: B 723 THR cc_start: 0.7927 (m) cc_final: 0.7530 (p) REVERT: B 738 LYS cc_start: 0.8269 (mtmm) cc_final: 0.8053 (mtmm) REVERT: B 750 LEU cc_start: 0.8165 (tp) cc_final: 0.7396 (pp) REVERT: A 33 MET cc_start: 0.7606 (mmm) cc_final: 0.7367 (mmt) REVERT: A 107 GLU cc_start: 0.7913 (tt0) cc_final: 0.7275 (tm-30) REVERT: A 130 ASP cc_start: 0.8324 (m-30) cc_final: 0.7886 (t0) REVERT: A 149 ASP cc_start: 0.7526 (t0) cc_final: 0.7213 (t0) REVERT: A 182 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7610 (pt0) REVERT: A 198 ARG cc_start: 0.8447 (ttm-80) cc_final: 0.7842 (ttm-80) REVERT: A 355 LEU cc_start: 0.7361 (tp) cc_final: 0.6996 (tp) REVERT: A 417 VAL cc_start: 0.7615 (t) cc_final: 0.7376 (p) REVERT: A 566 ASN cc_start: 0.8057 (t0) cc_final: 0.7396 (t0) REVERT: A 571 THR cc_start: 0.8458 (p) cc_final: 0.8241 (p) REVERT: A 692 MET cc_start: 0.8097 (mtm) cc_final: 0.7882 (mtp) REVERT: A 720 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7505 (mtmm) REVERT: A 751 GLU cc_start: 0.7153 (pm20) cc_final: 0.6876 (pm20) REVERT: A 759 MET cc_start: 0.8174 (mmm) cc_final: 0.7960 (mmp) outliers start: 42 outliers final: 29 residues processed: 283 average time/residue: 0.2878 time to fit residues: 107.7253 Evaluate side-chains 275 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 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 270 ASP 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 557 ASN Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 206 ILE 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 419 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 254 HIS A 344 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10499 Z= 0.224 Angle : 0.541 10.139 14227 Z= 0.277 Chirality : 0.040 0.177 1630 Planarity : 0.004 0.038 1852 Dihedral : 7.106 154.511 1511 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.00 % Favored : 97.92 % Rotamer: Outliers : 3.78 % Allowed : 18.27 % 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: 1.64 (0.23), residues: 1301 helix: 2.57 (0.19), residues: 666 sheet: 0.43 (0.38), residues: 182 loop : -0.95 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 137 HIS 0.004 0.001 HIS B 752 PHE 0.013 0.002 PHE A 334 TYR 0.017 0.001 TYR B 635 ARG 0.010 0.000 ARG A 163 *********************** 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 297 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 256 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: B 156 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7956 (mtt180) REVERT: B 201 LEU cc_start: 0.8624 (tp) cc_final: 0.7729 (mm) REVERT: B 205 GLU cc_start: 0.7081 (tt0) cc_final: 0.6804 (mp0) REVERT: B 207 ASP cc_start: 0.7385 (t0) cc_final: 0.7151 (t0) REVERT: B 229 ASN cc_start: 0.7606 (t0) cc_final: 0.6898 (p0) REVERT: B 242 GLN cc_start: 0.7363 (mm-40) cc_final: 0.6806 (tm-30) REVERT: B 302 MET cc_start: 0.7293 (ptm) cc_final: 0.6982 (ptt) REVERT: B 373 GLN cc_start: 0.7490 (mt0) cc_final: 0.7214 (mm110) REVERT: B 560 GLU cc_start: 0.7355 (tm-30) cc_final: 0.7021 (tm-30) REVERT: B 565 LEU cc_start: 0.7832 (mt) cc_final: 0.7614 (mt) REVERT: B 640 VAL cc_start: 0.8534 (t) cc_final: 0.8096 (m) REVERT: B 693 ASP cc_start: 0.8063 (t0) cc_final: 0.7819 (t0) REVERT: B 723 THR cc_start: 0.7884 (m) cc_final: 0.7494 (p) REVERT: B 738 LYS cc_start: 0.8279 (mtmm) cc_final: 0.7885 (mtmm) REVERT: B 750 LEU cc_start: 0.8193 (tp) cc_final: 0.7430 (pp) REVERT: A 107 GLU cc_start: 0.7965 (tt0) cc_final: 0.7309 (tm-30) REVERT: A 130 ASP cc_start: 0.8343 (m-30) cc_final: 0.7906 (t0) REVERT: A 149 ASP cc_start: 0.7552 (t0) cc_final: 0.7249 (t0) REVERT: A 166 MET cc_start: 0.7650 (tpp) cc_final: 0.7096 (tpp) REVERT: A 182 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7679 (pt0) REVERT: A 198 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.7982 (ttm-80) REVERT: A 355 LEU cc_start: 0.7310 (tp) cc_final: 0.6956 (tp) REVERT: A 417 VAL cc_start: 0.7614 (t) cc_final: 0.7384 (p) REVERT: A 566 ASN cc_start: 0.8028 (t0) cc_final: 0.7390 (t0) REVERT: A 571 THR cc_start: 0.8451 (p) cc_final: 0.8232 (p) REVERT: A 720 LYS cc_start: 0.7750 (mtpt) cc_final: 0.7499 (mtmm) outliers start: 41 outliers final: 32 residues processed: 278 average time/residue: 0.2967 time to fit residues: 107.4420 Evaluate side-chains 281 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 248 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 LEU 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 270 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 ASP 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 557 ASN Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 GLU 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 302 MET Chi-restraints excluded: chain A residue 315 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: 8.9990 chunk 114 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10499 Z= 0.333 Angle : 0.590 8.277 14227 Z= 0.301 Chirality : 0.042 0.166 1630 Planarity : 0.005 0.041 1852 Dihedral : 7.169 153.294 1511 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.15 % Favored : 97.77 % Rotamer: Outliers : 4.15 % Allowed : 18.36 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.23), residues: 1301 helix: 2.38 (0.19), residues: 660 sheet: 0.39 (0.39), residues: 180 loop : -1.06 (0.25), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 137 HIS 0.006 0.002 HIS A 760 PHE 0.027 0.002 PHE A 36 TYR 0.017 0.002 TYR A 635 ARG 0.007 0.001 ARG B 667 *********************** 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 308 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 263 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7341 (ttm-80) REVERT: B 157 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7899 (pp) REVERT: B 166 MET cc_start: 0.7864 (tpp) cc_final: 0.7537 (tpp) REVERT: B 201 LEU cc_start: 0.8636 (tp) cc_final: 0.7940 (tp) REVERT: B 205 GLU cc_start: 0.7173 (tt0) cc_final: 0.6877 (mp0) REVERT: B 207 ASP cc_start: 0.7420 (t0) cc_final: 0.7187 (t0) REVERT: B 229 ASN cc_start: 0.7681 (t0) cc_final: 0.6889 (p0) REVERT: B 242 GLN cc_start: 0.7375 (mm-40) cc_final: 0.6826 (tm-30) REVERT: B 302 MET cc_start: 0.7433 (ptm) cc_final: 0.7150 (ptt) REVERT: B 373 GLN cc_start: 0.7504 (mt0) cc_final: 0.7236 (mm110) REVERT: B 560 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7125 (tm-30) REVERT: B 640 VAL cc_start: 0.8532 (t) cc_final: 0.8094 (m) REVERT: B 693 ASP cc_start: 0.8114 (t0) cc_final: 0.7897 (t0) REVERT: B 738 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7999 (mtmm) REVERT: B 750 LEU cc_start: 0.8219 (tp) cc_final: 0.7588 (pp) REVERT: B 784 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6971 (tp30) REVERT: A 130 ASP cc_start: 0.8367 (m-30) cc_final: 0.7945 (t0) REVERT: A 149 ASP cc_start: 0.7643 (t0) cc_final: 0.7335 (t0) REVERT: A 166 MET cc_start: 0.7691 (tpp) cc_final: 0.7251 (tpp) REVERT: A 182 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7576 (pt0) REVERT: A 198 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.7724 (ttm-80) REVERT: A 355 LEU cc_start: 0.7336 (tp) cc_final: 0.6994 (tp) REVERT: A 417 VAL cc_start: 0.7644 (t) cc_final: 0.7423 (p) REVERT: A 566 ASN cc_start: 0.7980 (t0) cc_final: 0.7391 (t0) REVERT: A 571 THR cc_start: 0.8523 (p) cc_final: 0.8307 (p) REVERT: A 662 ASP cc_start: 0.6906 (m-30) cc_final: 0.6057 (p0) REVERT: A 720 LYS cc_start: 0.7779 (mtpt) cc_final: 0.7528 (mtmm) REVERT: A 751 GLU cc_start: 0.7571 (pm20) cc_final: 0.7339 (pm20) outliers start: 45 outliers final: 36 residues processed: 288 average time/residue: 0.3130 time to fit residues: 116.7131 Evaluate side-chains 294 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 255 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 LEU 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 265 ASP Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 ASP 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 557 ASN Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 674 MET 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 B residue 784 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 260 MET 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 419 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 574 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 734 GLN Chi-restraints excluded: chain A residue 748 ASP 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: 9.9990 chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10499 Z= 0.370 Angle : 0.608 9.031 14227 Z= 0.311 Chirality : 0.043 0.171 1630 Planarity : 0.005 0.047 1852 Dihedral : 7.216 153.013 1511 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.61 % Favored : 97.31 % Rotamer: Outliers : 4.15 % Allowed : 18.54 % Favored : 77.31 % 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: 1.15 (0.23), residues: 1301 helix: 2.17 (0.19), residues: 660 sheet: 0.34 (0.41), residues: 169 loop : -1.15 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 137 HIS 0.007 0.002 HIS A 585 PHE 0.031 0.002 PHE A 36 TYR 0.018 0.002 TYR B 635 ARG 0.009 0.001 ARG B 220 *********************** 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 317 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 272 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7500 (ttm-80) REVERT: B 156 ARG cc_start: 0.8186 (mtt180) cc_final: 0.7888 (mmt180) REVERT: B 166 MET cc_start: 0.7875 (tpp) cc_final: 0.7459 (tpp) REVERT: B 197 ARG cc_start: 0.8074 (mtp180) cc_final: 0.7874 (mtp180) REVERT: B 201 LEU cc_start: 0.8654 (tp) cc_final: 0.7977 (tp) REVERT: B 205 GLU cc_start: 0.7217 (tt0) cc_final: 0.6941 (mp0) REVERT: B 229 ASN cc_start: 0.7776 (t0) cc_final: 0.6964 (p0) REVERT: B 302 MET cc_start: 0.7368 (ptm) cc_final: 0.7095 (ptt) REVERT: B 373 GLN cc_start: 0.7521 (mt0) cc_final: 0.7259 (mm110) REVERT: B 393 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6382 (mp) REVERT: B 560 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7150 (tm-30) REVERT: B 640 VAL cc_start: 0.8558 (t) cc_final: 0.8113 (m) REVERT: B 693 ASP cc_start: 0.8118 (t0) cc_final: 0.7902 (t0) REVERT: B 723 THR cc_start: 0.7884 (m) cc_final: 0.7499 (p) REVERT: B 738 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7943 (mtmm) REVERT: B 750 LEU cc_start: 0.8255 (tp) cc_final: 0.7671 (pp) REVERT: B 784 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6979 (tp30) REVERT: A 33 MET cc_start: 0.7646 (mmm) cc_final: 0.7277 (mmt) REVERT: A 130 ASP cc_start: 0.8385 (m-30) cc_final: 0.7942 (t0) REVERT: A 149 ASP cc_start: 0.7697 (t0) cc_final: 0.7362 (t0) REVERT: A 166 MET cc_start: 0.7659 (tpp) cc_final: 0.7326 (tpp) REVERT: A 198 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.7968 (ttm-80) REVERT: A 355 LEU cc_start: 0.7361 (tp) cc_final: 0.7000 (tp) REVERT: A 417 VAL cc_start: 0.7683 (t) cc_final: 0.7482 (p) REVERT: A 566 ASN cc_start: 0.7972 (t0) cc_final: 0.7374 (t0) REVERT: A 571 THR cc_start: 0.8564 (p) cc_final: 0.8343 (p) REVERT: A 662 ASP cc_start: 0.6933 (m-30) cc_final: 0.6044 (p0) REVERT: A 720 LYS cc_start: 0.7788 (mtpt) cc_final: 0.7528 (mtmm) REVERT: A 751 GLU cc_start: 0.7590 (pm20) cc_final: 0.7320 (pm20) outliers start: 45 outliers final: 34 residues processed: 295 average time/residue: 0.3094 time to fit residues: 118.1271 Evaluate side-chains 300 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 264 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 265 ASP Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 393 LEU 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 645 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 674 MET 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 B residue 781 VAL Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 170 LEU 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 513 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 617 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 748 ASP 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: 0.0970 chunk 50 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 overall best weight: 2.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10499 Z= 0.232 Angle : 0.556 8.328 14227 Z= 0.285 Chirality : 0.039 0.140 1630 Planarity : 0.005 0.042 1852 Dihedral : 7.072 152.752 1511 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.85 % Rotamer: Outliers : 3.60 % Allowed : 19.46 % Favored : 76.94 % 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: 1.34 (0.23), residues: 1301 helix: 2.37 (0.20), residues: 661 sheet: 0.14 (0.39), residues: 184 loop : -1.07 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 137 HIS 0.005 0.001 HIS A 254 PHE 0.027 0.001 PHE A 36 TYR 0.020 0.001 TYR B 635 ARG 0.007 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 307 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 268 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7488 (ttm-80) REVERT: B 156 ARG cc_start: 0.8197 (mtt180) cc_final: 0.7903 (mmt180) REVERT: B 197 ARG cc_start: 0.8199 (mtp180) cc_final: 0.7990 (mtp180) REVERT: B 201 LEU cc_start: 0.8677 (tp) cc_final: 0.8020 (tp) REVERT: B 205 GLU cc_start: 0.7188 (tt0) cc_final: 0.6911 (mp0) REVERT: B 229 ASN cc_start: 0.7701 (t0) cc_final: 0.6863 (p0) REVERT: B 302 MET cc_start: 0.7273 (ptm) cc_final: 0.6962 (ptt) REVERT: B 373 GLN cc_start: 0.7512 (mt0) cc_final: 0.7245 (mm110) REVERT: B 560 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7169 (tm-30) REVERT: B 640 VAL cc_start: 0.8538 (t) cc_final: 0.8102 (m) REVERT: B 723 THR cc_start: 0.7920 (m) cc_final: 0.7553 (p) REVERT: B 738 LYS cc_start: 0.8144 (mtmm) cc_final: 0.7753 (mtmm) REVERT: B 750 LEU cc_start: 0.8220 (tp) cc_final: 0.7636 (pp) REVERT: A 130 ASP cc_start: 0.8374 (m-30) cc_final: 0.7958 (t0) REVERT: A 149 ASP cc_start: 0.7731 (t0) cc_final: 0.7386 (t0) REVERT: A 166 MET cc_start: 0.7642 (tpp) cc_final: 0.7363 (tpp) REVERT: A 198 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.7965 (ttm-80) REVERT: A 355 LEU cc_start: 0.7267 (tp) cc_final: 0.6906 (tp) REVERT: A 566 ASN cc_start: 0.7968 (t0) cc_final: 0.7410 (t0) REVERT: A 571 THR cc_start: 0.8510 (p) cc_final: 0.8283 (p) REVERT: A 662 ASP cc_start: 0.6881 (m-30) cc_final: 0.5998 (p0) REVERT: A 720 LYS cc_start: 0.7694 (mtpt) cc_final: 0.7456 (mtmm) REVERT: A 751 GLU cc_start: 0.7471 (pm20) cc_final: 0.7186 (pm20) outliers start: 39 outliers final: 34 residues processed: 290 average time/residue: 0.3083 time to fit residues: 116.1150 Evaluate side-chains 300 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 266 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 322 LEU Chi-restraints excluded: chain B residue 333 ASP 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 557 ASN Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 695 ILE 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 784 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 170 LEU 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 513 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 617 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 748 ASP 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: 4.9990 chunk 110 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10499 Z= 0.303 Angle : 0.587 8.557 14227 Z= 0.299 Chirality : 0.041 0.144 1630 Planarity : 0.005 0.043 1852 Dihedral : 7.097 152.096 1511 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.39 % Rotamer: Outliers : 3.69 % Allowed : 19.93 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.23), residues: 1301 helix: 2.25 (0.20), residues: 662 sheet: 0.08 (0.39), residues: 184 loop : -1.11 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 137 HIS 0.006 0.002 HIS A 585 PHE 0.014 0.002 PHE A 204 TYR 0.019 0.002 TYR B 635 ARG 0.008 0.001 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 305 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 265 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7541 (ttm-80) REVERT: B 156 ARG cc_start: 0.8219 (mtt180) cc_final: 0.7948 (mmt180) REVERT: B 166 MET cc_start: 0.7858 (tpp) cc_final: 0.7545 (tpp) REVERT: B 197 ARG cc_start: 0.8190 (mtp180) cc_final: 0.7975 (mtp180) REVERT: B 201 LEU cc_start: 0.8675 (tp) cc_final: 0.8241 (tp) REVERT: B 229 ASN cc_start: 0.7670 (t0) cc_final: 0.6955 (p0) REVERT: B 255 ILE cc_start: 0.7473 (mt) cc_final: 0.7220 (tt) REVERT: B 302 MET cc_start: 0.7319 (ptm) cc_final: 0.7025 (ptt) REVERT: B 373 GLN cc_start: 0.7510 (mt0) cc_final: 0.7240 (mm110) REVERT: B 560 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7173 (tm-30) REVERT: B 640 VAL cc_start: 0.8539 (t) cc_final: 0.8096 (m) REVERT: B 723 THR cc_start: 0.7848 (m) cc_final: 0.7455 (p) REVERT: B 738 LYS cc_start: 0.8150 (mtmm) cc_final: 0.7744 (mtmm) REVERT: B 750 LEU cc_start: 0.8267 (tp) cc_final: 0.7700 (pp) REVERT: A 33 MET cc_start: 0.7604 (mmm) cc_final: 0.7329 (mmm) REVERT: A 130 ASP cc_start: 0.8405 (m-30) cc_final: 0.8046 (t0) REVERT: A 149 ASP cc_start: 0.7748 (t0) cc_final: 0.7491 (t0) REVERT: A 166 MET cc_start: 0.7654 (tpp) cc_final: 0.7415 (tpp) REVERT: A 198 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.7944 (ttm-80) REVERT: A 355 LEU cc_start: 0.7286 (tp) cc_final: 0.6934 (tp) REVERT: A 566 ASN cc_start: 0.7918 (t0) cc_final: 0.7388 (t0) REVERT: A 571 THR cc_start: 0.8523 (p) cc_final: 0.8289 (p) REVERT: A 662 ASP cc_start: 0.7007 (m-30) cc_final: 0.6133 (p0) REVERT: A 720 LYS cc_start: 0.7622 (mtpt) cc_final: 0.7369 (mtmm) REVERT: A 751 GLU cc_start: 0.7483 (pm20) cc_final: 0.7191 (pm20) outliers start: 40 outliers final: 38 residues processed: 286 average time/residue: 0.2943 time to fit residues: 109.6871 Evaluate side-chains 298 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 260 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 LEU 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 322 LEU Chi-restraints excluded: chain B residue 333 ASP 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 557 ASN Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 674 MET 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 784 GLU 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 43 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 170 LEU 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 513 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 617 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 748 ASP 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: 6.9990 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10499 Z= 0.378 Angle : 0.638 14.089 14227 Z= 0.321 Chirality : 0.042 0.155 1630 Planarity : 0.005 0.047 1852 Dihedral : 7.185 151.384 1511 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.77 % Favored : 97.16 % Rotamer: Outliers : 3.41 % Allowed : 19.83 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.23), residues: 1301 helix: 2.07 (0.20), residues: 661 sheet: -0.00 (0.39), residues: 184 loop : -1.19 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 137 HIS 0.008 0.002 HIS A 585 PHE 0.017 0.002 PHE A 204 TYR 0.021 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 297 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 260 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7556 (ttm-80) REVERT: B 156 ARG cc_start: 0.8216 (mtt180) cc_final: 0.7945 (mmt180) REVERT: B 166 MET cc_start: 0.8004 (tpp) cc_final: 0.7655 (tpp) REVERT: B 197 ARG cc_start: 0.8187 (mtp180) cc_final: 0.7970 (mtp180) REVERT: B 202 TRP cc_start: 0.8135 (p-90) cc_final: 0.7822 (p-90) REVERT: B 205 GLU cc_start: 0.6989 (mp0) cc_final: 0.6506 (mp0) REVERT: B 229 ASN cc_start: 0.7692 (t0) cc_final: 0.6897 (p0) REVERT: B 255 ILE cc_start: 0.7533 (mt) cc_final: 0.7291 (tt) REVERT: B 302 MET cc_start: 0.7386 (ptm) cc_final: 0.7116 (ptt) REVERT: B 373 GLN cc_start: 0.7508 (mt0) cc_final: 0.7239 (mm110) REVERT: B 560 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7180 (tm-30) REVERT: B 635 TYR cc_start: 0.8215 (m-80) cc_final: 0.7894 (m-80) REVERT: B 640 VAL cc_start: 0.8535 (t) cc_final: 0.8112 (m) REVERT: B 723 THR cc_start: 0.7858 (m) cc_final: 0.7474 (p) REVERT: B 738 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7761 (mtmm) REVERT: B 750 LEU cc_start: 0.8274 (tp) cc_final: 0.7725 (pp) REVERT: B 784 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7005 (tp30) REVERT: A 130 ASP cc_start: 0.8395 (m-30) cc_final: 0.8080 (t0) REVERT: A 166 MET cc_start: 0.7671 (tpp) cc_final: 0.7435 (tpp) REVERT: A 198 ARG cc_start: 0.8336 (ttm-80) cc_final: 0.7917 (ttm-80) REVERT: A 355 LEU cc_start: 0.7348 (tp) cc_final: 0.6996 (tp) REVERT: A 566 ASN cc_start: 0.7829 (t0) cc_final: 0.7349 (t0) REVERT: A 571 THR cc_start: 0.8552 (p) cc_final: 0.8340 (p) REVERT: A 662 ASP cc_start: 0.7041 (m-30) cc_final: 0.6179 (p0) REVERT: A 720 LYS cc_start: 0.7599 (mtpt) cc_final: 0.7348 (mtmm) REVERT: A 751 GLU cc_start: 0.7506 (pm20) cc_final: 0.7217 (pm20) outliers start: 37 outliers final: 36 residues processed: 279 average time/residue: 0.3091 time to fit residues: 111.8434 Evaluate side-chains 295 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 258 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 LEU 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 322 LEU Chi-restraints excluded: chain B residue 333 ASP 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 557 ASN Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 674 MET 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 784 GLU 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 43 ASP Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 170 LEU 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 513 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 617 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 748 ASP 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: 10.0000 chunk 95 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 13 optimal weight: 0.0770 chunk 19 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110359 restraints weight = 19452.022| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.37 r_work: 0.3252 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 0.033 10499 Z= 0.216 Angle : 0.574 15.457 14227 Z= 0.289 Chirality : 0.039 0.146 1630 Planarity : 0.005 0.042 1852 Dihedral : 7.058 151.966 1511 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.15 % Favored : 97.77 % Rotamer: Outliers : 3.32 % Allowed : 20.11 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.23), residues: 1301 helix: 2.37 (0.20), residues: 661 sheet: 0.07 (0.40), residues: 184 loop : -1.10 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 137 HIS 0.005 0.001 HIS A 254 PHE 0.009 0.001 PHE A 204 TYR 0.015 0.001 TYR A 31 ARG 0.008 0.000 ARG B 220 =============================================================================== Job complete usr+sys time: 2718.72 seconds wall clock time: 48 minutes 42.36 seconds (2922.36 seconds total)