Starting phenix.real_space_refine on Fri Jul 3 04:57:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ai7_11793/07_2026/7ai7_11793.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ai7_11793/07_2026/7ai7_11793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ai7_11793/07_2026/7ai7_11793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ai7_11793/07_2026/7ai7_11793.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ai7_11793/07_2026/7ai7_11793.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ai7_11793/07_2026/7ai7_11793.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ai7_11793/07_2026/7ai7_11793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ai7_11793/07_2026/7ai7_11793.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 53 5.16 5 C 7492 2.51 5 N 2160 2.21 5 O 2349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12085 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6218 Classifications: {'peptide': 791} Link IDs: {'PTRANS': 35, 'TRANS': 755} Chain: "B" Number of atoms: 5261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5261 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 27, 'TRANS': 641} Chain: "C" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 266 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain breaks: 1 Chain: "D" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 286 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.56, per 1000 atoms: 0.21 Number of scatterers: 12085 At special positions: 0 Unit cell: (112.32, 114.66, 120.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 P 31 15.00 O 2349 8.00 N 2160 7.00 C 7492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 444.2 milliseconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2732 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 52.4% alpha, 12.3% beta 8 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.577A pdb=" N GLN A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 52 removed outlier: 3.918A pdb=" N LYS A 45 " --> pdb=" O TYR A 41 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 85 removed outlier: 3.608A pdb=" N LYS A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 174 removed outlier: 3.578A pdb=" N MET A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 removed outlier: 4.353A pdb=" N ILE A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 230 through 249 removed outlier: 3.555A pdb=" N LEU A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.541A pdb=" N VAL A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 312 removed outlier: 4.226A pdb=" N ARG A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET A 306 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.512A pdb=" N LEU A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 344 Proline residue: A 340 - end of helix removed outlier: 3.846A pdb=" N GLN A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 361 through 385 removed outlier: 3.504A pdb=" N LEU A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) Proline residue: A 376 - end of helix removed outlier: 3.714A pdb=" N THR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.784A 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 430 through 459 removed outlier: 4.044A pdb=" N ASP A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 448 " --> pdb=" O THR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 removed outlier: 4.088A pdb=" N HIS A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 483' Processing helix chain 'A' and resid 503 through 536 removed outlier: 3.593A pdb=" N GLU A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 565 Processing helix chain 'A' and resid 585 through 592 removed outlier: 3.674A pdb=" N GLN A 590 " --> pdb=" O PRO A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 636 removed outlier: 3.599A pdb=" N THR A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA A 628 " --> pdb=" O MET A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 684 removed outlier: 3.506A pdb=" N GLU A 673 " --> pdb=" O THR A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 718 Processing helix chain 'A' and resid 731 through 733 No H-bonds generated for 'chain 'A' and resid 731 through 733' Processing helix chain 'A' and resid 734 through 739 removed outlier: 3.553A pdb=" N LYS A 738 " --> pdb=" O GLN A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 778 Processing helix chain 'A' and resid 782 through 798 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.602A pdb=" N MET B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 192 removed outlier: 4.217A pdb=" N ILE B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 205 through 218 removed outlier: 3.624A pdb=" N ARG B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 248 removed outlier: 3.564A pdb=" N LEU B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 277 Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.549A pdb=" N VAL B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 removed outlier: 3.793A pdb=" N ARG B 305 " --> pdb=" O PRO B 301 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 306 " --> pdb=" O MET B 302 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 331 removed outlier: 3.678A pdb=" N LEU B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 344 Proline residue: B 340 - end of helix removed outlier: 3.869A pdb=" N GLN B 344 " --> pdb=" O PRO B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 361 through 385 removed outlier: 3.537A pdb=" N LEU B 365 " --> pdb=" O ARG B 361 " (cutoff:3.500A) Proline residue: B 376 - end of helix removed outlier: 3.718A pdb=" N THR B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 398 removed outlier: 3.789A 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 459 removed outlier: 3.920A pdb=" N ASP B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 483 removed outlier: 3.982A pdb=" N HIS B 483 " --> pdb=" O ARG B 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 479 through 483' Processing helix chain 'B' and resid 503 through 536 removed outlier: 3.793A pdb=" N PHE B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 565 Processing helix chain 'B' and resid 585 through 592 removed outlier: 3.544A pdb=" N GLN B 590 " --> pdb=" O PRO B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 636 removed outlier: 4.022A pdb=" N THR B 627 " --> pdb=" O TYR B 623 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA B 628 " --> pdb=" O MET B 624 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 771 through 778 Processing helix chain 'B' and resid 782 through 798 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 3.502A pdb=" N TYR A 31 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE A 40 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU A 29 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU A 28 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N CYS A 93 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE A 30 " --> pdb=" O CYS A 93 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 112 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 158 removed outlier: 6.011A pdb=" N LEU A 132 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU A 179 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA A 134 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N ALA A 181 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ILE A 136 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 468 removed outlier: 3.501A pdb=" N GLN A 493 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 599 through 603 removed outlier: 5.413A pdb=" N ASN A 599 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 582 " --> pdb=" O ASN A 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 653 through 657 removed outlier: 3.608A pdb=" N ASP A 693 " --> pdb=" O ARG A 656 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A 690 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ALA A 726 " --> pdb=" O VAL A 690 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N MET A 692 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU A 610 " --> pdb=" O PHE A 725 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET A 609 " --> pdb=" O ALA A 743 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL A 745 " --> pdb=" O MET A 609 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE A 611 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU A 747 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN A 763 " --> pdb=" O HIS A 746 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP A 748 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER A 761 " --> pdb=" O ASP A 748 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N LEU A 750 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N MET A 759 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 196 through 199 removed outlier: 4.203A pdb=" N GLU B 177 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 181 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLN B 138 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE B 155 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 464 through 468 removed outlier: 3.537A pdb=" N GLN B 493 " --> pdb=" O ARG B 500 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 502 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG B 491 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 599 through 603 removed outlier: 5.535A pdb=" N ASN B 599 " --> pdb=" O GLU B 582 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU B 582 " --> pdb=" O ASN B 599 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 653 through 656 removed outlier: 7.073A pdb=" N PHE B 654 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N MET B 609 " --> pdb=" O ALA B 743 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL B 745 " --> pdb=" O MET B 609 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE B 611 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 747 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 763 " --> pdb=" O HIS B 746 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B 748 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER B 761 " --> pdb=" O ASP B 748 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N LEU B 750 " --> pdb=" O MET B 759 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N MET B 759 " --> pdb=" O LEU B 750 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.29: 1984 1.29 - 1.44: 3218 1.44 - 1.59: 6995 1.59 - 1.74: 53 1.74 - 1.89: 95 Bond restraints: 12345 Sorted by residual: bond pdb=" C PRO A 314 " pdb=" O PRO A 314 " ideal model delta sigma weight residual 1.235 1.144 0.092 1.30e-02 5.92e+03 4.96e+01 bond pdb=" C VAL A 745 " pdb=" O VAL A 745 " ideal model delta sigma weight residual 1.235 1.305 -0.070 1.02e-02 9.61e+03 4.71e+01 bond pdb=" C LEU A 307 " pdb=" O LEU A 307 " ideal model delta sigma weight residual 1.236 1.154 0.082 1.29e-02 6.01e+03 4.05e+01 bond pdb=" C LYS A 464 " pdb=" O LYS A 464 " ideal model delta sigma weight residual 1.235 1.166 0.069 1.14e-02 7.69e+03 3.72e+01 bond pdb=" C SER A 770 " pdb=" O SER A 770 " ideal model delta sigma weight residual 1.236 1.310 -0.074 1.22e-02 6.72e+03 3.69e+01 ... (remaining 12340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 13323 2.46 - 4.92: 3216 4.92 - 7.38: 272 7.38 - 9.84: 19 9.84 - 12.30: 3 Bond angle restraints: 16833 Sorted by residual: angle pdb=" N ILE A 636 " pdb=" CA ILE A 636 " pdb=" C ILE A 636 " ideal model delta sigma weight residual 112.29 105.02 7.27 9.40e-01 1.13e+00 5.99e+01 angle pdb=" N GLU A 451 " pdb=" CA GLU A 451 " pdb=" C GLU A 451 " ideal model delta sigma weight residual 112.23 104.14 8.09 1.26e+00 6.30e-01 4.12e+01 angle pdb=" CA SER B 478 " pdb=" C SER B 478 " pdb=" O SER B 478 " ideal model delta sigma weight residual 121.56 114.62 6.94 1.09e+00 8.42e-01 4.05e+01 angle pdb=" N CYS A 297 " pdb=" CA CYS A 297 " pdb=" C CYS A 297 " ideal model delta sigma weight residual 112.92 105.17 7.75 1.23e+00 6.61e-01 3.97e+01 angle pdb=" CA GLY A 658 " pdb=" C GLY A 658 " pdb=" O GLY A 658 " ideal model delta sigma weight residual 122.29 117.19 5.10 8.10e-01 1.52e+00 3.96e+01 ... (remaining 16828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.79: 7108 33.79 - 67.58: 357 67.58 - 101.38: 17 101.38 - 135.17: 2 135.17 - 168.96: 2 Dihedral angle restraints: 7486 sinusoidal: 3250 harmonic: 4236 Sorted by residual: dihedral pdb=" C5' ADP B1801 " pdb=" O5' ADP B1801 " pdb=" PA ADP B1801 " pdb=" O2A ADP B1801 " ideal model delta sinusoidal sigma weight residual -60.00 108.97 -168.96 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP A1801 " pdb=" O3A ADP A1801 " pdb=" PA ADP A1801 " pdb=" PB ADP A1801 " ideal model delta sinusoidal sigma weight residual -60.00 94.44 -154.44 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" O1B ADP B1801 " pdb=" O3A ADP B1801 " pdb=" PB ADP B1801 " pdb=" PA ADP B1801 " ideal model delta sinusoidal sigma weight residual -60.00 -179.29 119.29 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 7483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 974 0.070 - 0.140: 657 0.140 - 0.211: 211 0.211 - 0.281: 45 0.281 - 0.351: 25 Chirality restraints: 1912 Sorted by residual: chirality pdb=" CA ILE B 503 " pdb=" N ILE B 503 " pdb=" C ILE B 503 " pdb=" CB ILE B 503 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA LEU A 724 " pdb=" N LEU A 724 " pdb=" C LEU A 724 " pdb=" CB LEU A 724 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB THR A 335 " pdb=" CA THR A 335 " pdb=" OG1 THR A 335 " pdb=" CG2 THR A 335 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 1909 not shown) Planarity restraints: 2104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 137 " 0.001 2.00e-02 2.50e+03 2.85e-02 2.03e+01 pdb=" CG TRP A 137 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP A 137 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 137 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP A 137 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TRP A 137 " 0.055 2.00e-02 2.50e+03 pdb=" CE3 TRP A 137 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 137 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 137 " -0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP A 137 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 179 " -0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C LEU A 179 " 0.075 2.00e-02 2.50e+03 pdb=" O LEU A 179 " -0.028 2.00e-02 2.50e+03 pdb=" N TYR A 180 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 149 " -0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C ASP A 149 " 0.074 2.00e-02 2.50e+03 pdb=" O ASP A 149 " -0.027 2.00e-02 2.50e+03 pdb=" N ILE A 150 " -0.026 2.00e-02 2.50e+03 ... (remaining 2101 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 4228 2.92 - 3.42: 12148 3.42 - 3.91: 21422 3.91 - 4.41: 23923 4.41 - 4.90: 38888 Nonbonded interactions: 100609 Sorted by model distance: nonbonded pdb=" O5' DG D 10 " pdb=" O4' DG D 10 " model vdw 2.425 2.432 nonbonded pdb=" OD1 ASP A 207 " pdb=" N THR A 208 " model vdw 2.427 3.120 nonbonded pdb=" O GLY A 442 " pdb=" OD1 ASP A 445 " model vdw 2.436 3.040 nonbonded pdb=" O5' DA C 44 " pdb=" O4' DA C 44 " model vdw 2.438 2.432 nonbonded pdb=" N TYR A 180 " pdb=" O TYR A 180 " model vdw 2.448 2.496 ... (remaining 100604 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.250 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.015 0.109 12345 Z= 1.127 Angle : 1.972 12.301 16833 Z= 1.445 Chirality : 0.101 0.351 1912 Planarity : 0.008 0.043 2104 Dihedral : 18.071 168.962 4754 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.99 % Allowed : 9.83 % Favored : 89.17 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.19), residues: 1456 helix: -1.03 (0.17), residues: 658 sheet: -2.08 (0.34), residues: 197 loop : -2.02 (0.21), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.002 ARG A 156 TYR 0.039 0.005 TYR A 623 PHE 0.054 0.006 PHE A 204 TRP 0.055 0.007 TRP A 137 HIS 0.025 0.005 HIS A 752 Details of bonding type rmsd/Z covalent geometry : bond 0.01501 / 1.13 (12345) covalent geometry : angle 1.97223 / 1.44 (16833) hydrogen bonds : bond 0.23230 / 15.84 ( 590) hydrogen bonds : angle 9.59541 / 6.60 ( 1710) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ASN cc_start: 0.7444 (t0) cc_final: 0.6784 (t0) REVERT: A 609 MET cc_start: 0.7896 (ttm) cc_final: 0.7662 (ttm) REVERT: B 184 PHE cc_start: 0.5075 (t80) cc_final: 0.4695 (t80) REVERT: B 347 ASP cc_start: 0.7794 (p0) cc_final: 0.7109 (p0) REVERT: B 430 ASN cc_start: 0.8473 (t0) cc_final: 0.7523 (t0) REVERT: B 694 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6593 (tp30) outliers start: 12 outliers final: 0 residues processed: 183 average time/residue: 0.1310 time to fit residues: 32.7474 Evaluate side-chains 101 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 694 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 GLN B 476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.084110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.062915 restraints weight = 47347.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.064536 restraints weight = 27072.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.066121 restraints weight = 16819.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.065983 restraints weight = 14485.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.065937 restraints weight = 12226.101| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 12345 Z= 0.170 Angle : 0.727 10.969 16833 Z= 0.376 Chirality : 0.044 0.257 1912 Planarity : 0.005 0.043 2104 Dihedral : 16.898 166.637 1943 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.40 % Allowed : 13.88 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.21), residues: 1456 helix: 0.36 (0.18), residues: 698 sheet: -1.44 (0.36), residues: 207 loop : -1.30 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 420 TYR 0.024 0.002 TYR A 473 PHE 0.015 0.002 PHE A 143 TRP 0.007 0.001 TRP B 202 HIS 0.005 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (12345) covalent geometry : angle 0.72708 / 0.38 (16833) hydrogen bonds : bond 0.06331 / 4.22 ( 590) hydrogen bonds : angle 5.74839 / 3.92 ( 1710) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.7538 (ptt) cc_final: 0.7326 (ptt) REVERT: A 33 MET cc_start: 0.8899 (tpp) cc_final: 0.8649 (tpp) REVERT: A 165 THR cc_start: 0.7746 (m) cc_final: 0.7539 (p) REVERT: A 361 ARG cc_start: 0.6605 (mtt180) cc_final: 0.6356 (mtt180) REVERT: A 430 ASN cc_start: 0.7234 (t0) cc_final: 0.6706 (t0) REVERT: B 166 MET cc_start: 0.8127 (mmm) cc_final: 0.7746 (mmm) REVERT: B 184 PHE cc_start: 0.6203 (t80) cc_final: 0.5136 (t80) REVERT: B 306 MET cc_start: 0.7616 (tpp) cc_final: 0.7398 (tpp) REVERT: B 347 ASP cc_start: 0.7786 (p0) cc_final: 0.7259 (p0) REVERT: B 430 ASN cc_start: 0.8582 (t0) cc_final: 0.8235 (t0) REVERT: B 432 GLU cc_start: 0.8966 (mp0) cc_final: 0.8763 (mp0) REVERT: B 490 MET cc_start: 0.8507 (tmm) cc_final: 0.8279 (tmm) outliers start: 17 outliers final: 5 residues processed: 117 average time/residue: 0.1104 time to fit residues: 18.4607 Evaluate side-chains 89 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 414 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 25 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 GLN A 493 GLN A 557 ASN A 760 HIS B 391 GLN B 526 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.083328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.062046 restraints weight = 47941.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.063627 restraints weight = 26993.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.064150 restraints weight = 17303.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.064464 restraints weight = 16519.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.064446 restraints weight = 14063.248| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12345 Z= 0.140 Angle : 0.652 11.981 16833 Z= 0.332 Chirality : 0.042 0.244 1912 Planarity : 0.005 0.046 2104 Dihedral : 16.526 166.777 1940 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.65 % Allowed : 16.53 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.21), residues: 1456 helix: 0.72 (0.19), residues: 702 sheet: -1.04 (0.38), residues: 183 loop : -1.19 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 163 TYR 0.027 0.002 TYR A 473 PHE 0.011 0.001 PHE A 204 TRP 0.005 0.001 TRP B 709 HIS 0.004 0.001 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (12345) covalent geometry : angle 0.65184 / 0.33 (16833) hydrogen bonds : bond 0.05232 / 3.47 ( 590) hydrogen bonds : angle 5.18831 / 3.56 ( 1710) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.9034 (tpp) cc_final: 0.8728 (tpp) REVERT: A 364 ASP cc_start: 0.7968 (m-30) cc_final: 0.7768 (m-30) REVERT: A 430 ASN cc_start: 0.7231 (t0) cc_final: 0.6817 (t0) REVERT: A 633 MET cc_start: 0.8192 (mtp) cc_final: 0.7971 (mtp) REVERT: A 671 MET cc_start: 0.7708 (tpp) cc_final: 0.7428 (tpp) REVERT: B 166 MET cc_start: 0.8344 (mmm) cc_final: 0.7869 (mmm) REVERT: B 187 MET cc_start: 0.8650 (mmm) cc_final: 0.8207 (mmp) REVERT: B 347 ASP cc_start: 0.7680 (p0) cc_final: 0.7230 (p0) REVERT: B 430 ASN cc_start: 0.8732 (t0) cc_final: 0.8492 (t0) REVERT: B 490 MET cc_start: 0.8666 (tmm) cc_final: 0.8454 (tmm) outliers start: 20 outliers final: 8 residues processed: 105 average time/residue: 0.1021 time to fit residues: 15.5497 Evaluate side-chains 85 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 727 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 120 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN B 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.082417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.061129 restraints weight = 47474.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.062476 restraints weight = 26285.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.063094 restraints weight = 18124.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063389 restraints weight = 16590.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063396 restraints weight = 14243.024| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12345 Z= 0.145 Angle : 0.637 9.660 16833 Z= 0.323 Chirality : 0.042 0.282 1912 Planarity : 0.004 0.048 2104 Dihedral : 16.306 160.254 1940 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.31 % Allowed : 16.78 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1456 helix: 0.92 (0.19), residues: 708 sheet: -0.80 (0.40), residues: 171 loop : -1.11 (0.23), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 163 TYR 0.039 0.002 TYR B 509 PHE 0.008 0.001 PHE B 532 TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (12345) covalent geometry : angle 0.63688 / 0.32 (16833) hydrogen bonds : bond 0.04802 / 3.21 ( 590) hydrogen bonds : angle 4.98167 / 3.41 ( 1710) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.8989 (tpp) cc_final: 0.8731 (tpp) REVERT: A 430 ASN cc_start: 0.7081 (t0) cc_final: 0.6489 (t0) REVERT: A 471 HIS cc_start: 0.8727 (m170) cc_final: 0.8450 (m170) REVERT: A 739 MET cc_start: 0.6765 (ttt) cc_final: 0.6309 (ttt) REVERT: B 166 MET cc_start: 0.8656 (mmm) cc_final: 0.8042 (mmm) REVERT: B 347 ASP cc_start: 0.7507 (p0) cc_final: 0.7017 (p0) REVERT: B 430 ASN cc_start: 0.8729 (t0) cc_final: 0.8458 (t0) REVERT: B 432 GLU cc_start: 0.9032 (mp0) cc_final: 0.8747 (mp0) REVERT: B 490 MET cc_start: 0.8767 (tmm) cc_final: 0.8543 (tmm) outliers start: 28 outliers final: 13 residues processed: 104 average time/residue: 0.1322 time to fit residues: 19.7283 Evaluate side-chains 95 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 727 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 69 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 599 ASN A 626 GLN B 339 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.078717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.056792 restraints weight = 48456.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.058152 restraints weight = 28154.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.058760 restraints weight = 19112.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.058752 restraints weight = 18068.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.058893 restraints weight = 16569.167| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12345 Z= 0.274 Angle : 0.747 9.336 16833 Z= 0.380 Chirality : 0.046 0.182 1912 Planarity : 0.005 0.052 2104 Dihedral : 16.287 154.241 1940 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.74 % Allowed : 17.11 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.21), residues: 1456 helix: 0.68 (0.18), residues: 711 sheet: -0.83 (0.39), residues: 171 loop : -1.24 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 584 TYR 0.039 0.002 TYR A 635 PHE 0.012 0.002 PHE A 467 TRP 0.007 0.001 TRP A 709 HIS 0.012 0.002 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.27 (12345) covalent geometry : angle 0.74704 / 0.38 (16833) hydrogen bonds : bond 0.05272 / 3.52 ( 590) hydrogen bonds : angle 5.09873 / 3.51 ( 1710) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.9045 (tpp) cc_final: 0.8749 (tpp) REVERT: A 471 HIS cc_start: 0.8936 (m170) cc_final: 0.8676 (m170) REVERT: A 535 LEU cc_start: 0.9149 (mp) cc_final: 0.8757 (tt) REVERT: A 633 MET cc_start: 0.8542 (mtp) cc_final: 0.8187 (mtp) REVERT: B 166 MET cc_start: 0.8804 (mmm) cc_final: 0.8128 (mmm) REVERT: B 347 ASP cc_start: 0.7742 (p0) cc_final: 0.7319 (p0) REVERT: B 430 ASN cc_start: 0.8791 (t0) cc_final: 0.8568 (t0) REVERT: B 490 MET cc_start: 0.8768 (tmm) cc_final: 0.8555 (tmm) outliers start: 21 outliers final: 12 residues processed: 99 average time/residue: 0.1292 time to fit residues: 18.4011 Evaluate side-chains 89 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 785 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 91 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 114 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 339 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.080094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.058533 restraints weight = 48065.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.059879 restraints weight = 26844.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.060490 restraints weight = 18442.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.060614 restraints weight = 17447.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.060707 restraints weight = 15416.782| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12345 Z= 0.153 Angle : 0.631 10.668 16833 Z= 0.322 Chirality : 0.043 0.283 1912 Planarity : 0.004 0.046 2104 Dihedral : 16.206 152.754 1940 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.82 % Allowed : 17.44 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1456 helix: 0.95 (0.19), residues: 713 sheet: -0.73 (0.40), residues: 171 loop : -1.19 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 163 TYR 0.020 0.001 TYR B 635 PHE 0.010 0.001 PHE A 467 TRP 0.005 0.001 TRP A 709 HIS 0.004 0.001 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (12345) covalent geometry : angle 0.63106 / 0.32 (16833) hydrogen bonds : bond 0.04583 / 3.04 ( 590) hydrogen bonds : angle 4.89849 / 3.38 ( 1710) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.8952 (tpp) cc_final: 0.8669 (tpp) REVERT: A 535 LEU cc_start: 0.9110 (mp) cc_final: 0.8731 (tt) REVERT: A 633 MET cc_start: 0.8296 (mtp) cc_final: 0.7924 (mtp) REVERT: B 166 MET cc_start: 0.8876 (mmm) cc_final: 0.8134 (mmm) REVERT: B 184 PHE cc_start: 0.6648 (t80) cc_final: 0.5806 (t80) REVERT: B 347 ASP cc_start: 0.7641 (p0) cc_final: 0.7222 (p0) REVERT: B 430 ASN cc_start: 0.8741 (t0) cc_final: 0.8517 (t0) REVERT: B 490 MET cc_start: 0.8813 (tmm) cc_final: 0.8600 (tmm) outliers start: 22 outliers final: 13 residues processed: 92 average time/residue: 0.1335 time to fit residues: 17.4773 Evaluate side-chains 92 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 727 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 113 optimal weight: 0.2980 chunk 63 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 HIS B 557 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.079843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058625 restraints weight = 48396.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.059659 restraints weight = 27585.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.060218 restraints weight = 20206.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.060570 restraints weight = 17772.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.060577 restraints weight = 15126.183| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12345 Z= 0.160 Angle : 0.634 11.638 16833 Z= 0.321 Chirality : 0.043 0.215 1912 Planarity : 0.004 0.046 2104 Dihedral : 16.083 148.956 1940 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.82 % Allowed : 17.36 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1456 helix: 1.03 (0.19), residues: 713 sheet: -0.81 (0.38), residues: 186 loop : -1.18 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 449 TYR 0.017 0.001 TYR A 635 PHE 0.011 0.001 PHE A 467 TRP 0.006 0.001 TRP B 436 HIS 0.007 0.001 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (12345) covalent geometry : angle 0.63429 / 0.32 (16833) hydrogen bonds : bond 0.04485 / 3.00 ( 590) hydrogen bonds : angle 4.79586 / 3.30 ( 1710) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8839 (tpp) cc_final: 0.8517 (tpp) REVERT: A 33 MET cc_start: 0.8907 (tpp) cc_final: 0.8586 (tpp) REVERT: B 166 MET cc_start: 0.8926 (mmm) cc_final: 0.8133 (mmm) REVERT: B 184 PHE cc_start: 0.6637 (t80) cc_final: 0.5785 (t80) REVERT: B 347 ASP cc_start: 0.7641 (p0) cc_final: 0.7263 (p0) REVERT: B 430 ASN cc_start: 0.8701 (t0) cc_final: 0.8449 (t0) REVERT: B 432 GLU cc_start: 0.9007 (mp0) cc_final: 0.8770 (mp0) REVERT: B 490 MET cc_start: 0.8805 (tmm) cc_final: 0.8592 (tmm) outliers start: 22 outliers final: 15 residues processed: 91 average time/residue: 0.1372 time to fit residues: 17.6553 Evaluate side-chains 91 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 727 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 20 optimal weight: 9.9990 chunk 57 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 17 optimal weight: 30.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.080423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.059462 restraints weight = 47979.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.060383 restraints weight = 26303.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.061591 restraints weight = 18856.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.061636 restraints weight = 16779.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.061616 restraints weight = 14158.656| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12345 Z= 0.129 Angle : 0.624 15.745 16833 Z= 0.311 Chirality : 0.042 0.212 1912 Planarity : 0.004 0.044 2104 Dihedral : 15.954 145.388 1940 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.57 % Allowed : 17.52 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1456 helix: 1.08 (0.19), residues: 720 sheet: -0.75 (0.40), residues: 174 loop : -1.19 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 275 TYR 0.017 0.001 TYR B 635 PHE 0.011 0.001 PHE A 467 TRP 0.006 0.001 TRP B 436 HIS 0.004 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (12345) covalent geometry : angle 0.62384 / 0.31 (16833) hydrogen bonds : bond 0.04251 / 2.83 ( 590) hydrogen bonds : angle 4.69026 / 3.22 ( 1710) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.8845 (tpp) cc_final: 0.8509 (tpp) REVERT: A 535 LEU cc_start: 0.9054 (mp) cc_final: 0.8713 (tt) REVERT: A 790 ARG cc_start: 0.6544 (mmt180) cc_final: 0.6271 (mmt180) REVERT: B 166 MET cc_start: 0.8922 (mmm) cc_final: 0.8136 (mmm) REVERT: B 184 PHE cc_start: 0.6646 (t80) cc_final: 0.5834 (t80) REVERT: B 347 ASP cc_start: 0.7581 (p0) cc_final: 0.7185 (p0) REVERT: B 430 ASN cc_start: 0.8644 (t0) cc_final: 0.8430 (t0) REVERT: B 432 GLU cc_start: 0.8979 (mp0) cc_final: 0.8727 (mp0) REVERT: B 624 MET cc_start: 0.8357 (mmm) cc_final: 0.8064 (mmm) outliers start: 19 outliers final: 11 residues processed: 88 average time/residue: 0.1314 time to fit residues: 16.5612 Evaluate side-chains 88 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 727 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 58 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.0050 chunk 107 optimal weight: 0.0030 chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 47 optimal weight: 0.0060 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.3420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 HIS B 557 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.081753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.060981 restraints weight = 47724.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.062149 restraints weight = 26064.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.063128 restraints weight = 17946.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.063230 restraints weight = 17123.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.063227 restraints weight = 13862.343| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 12345 Z= 0.116 Angle : 0.611 13.044 16833 Z= 0.302 Chirality : 0.041 0.172 1912 Planarity : 0.004 0.044 2104 Dihedral : 15.800 136.722 1940 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.24 % Allowed : 18.35 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.22), residues: 1456 helix: 1.23 (0.19), residues: 723 sheet: -0.80 (0.39), residues: 181 loop : -1.12 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 275 TYR 0.014 0.001 TYR B 635 PHE 0.012 0.001 PHE A 467 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS A 728 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (12345) covalent geometry : angle 0.61088 / 0.30 (16833) hydrogen bonds : bond 0.03868 / 2.60 ( 590) hydrogen bonds : angle 4.53688 / 3.11 ( 1710) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.7300 (mtm) cc_final: 0.6749 (mmp) REVERT: A 33 MET cc_start: 0.8852 (tpp) cc_final: 0.8524 (tpp) REVERT: A 535 LEU cc_start: 0.8996 (mp) cc_final: 0.8672 (tt) REVERT: B 166 MET cc_start: 0.9007 (mmm) cc_final: 0.8286 (mmm) REVERT: B 184 PHE cc_start: 0.6724 (t80) cc_final: 0.5902 (t80) REVERT: B 347 ASP cc_start: 0.7436 (p0) cc_final: 0.7054 (p0) REVERT: B 430 ASN cc_start: 0.8619 (t0) cc_final: 0.8411 (t0) REVERT: B 432 GLU cc_start: 0.8977 (mp0) cc_final: 0.8724 (mp0) REVERT: B 624 MET cc_start: 0.8364 (mmm) cc_final: 0.8107 (mmm) REVERT: B 792 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.8972 (tptt) outliers start: 15 outliers final: 5 residues processed: 98 average time/residue: 0.1372 time to fit residues: 18.9505 Evaluate side-chains 84 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 792 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 103 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 56 optimal weight: 0.0870 chunk 102 optimal weight: 1.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 471 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.080186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.059535 restraints weight = 48005.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.060145 restraints weight = 27563.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.060360 restraints weight = 20835.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.060663 restraints weight = 20199.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.060623 restraints weight = 17907.471| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12345 Z= 0.163 Angle : 0.655 13.643 16833 Z= 0.323 Chirality : 0.042 0.303 1912 Planarity : 0.004 0.045 2104 Dihedral : 15.799 136.367 1940 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.99 % Allowed : 18.76 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.22), residues: 1456 helix: 1.14 (0.19), residues: 721 sheet: -0.69 (0.40), residues: 168 loop : -1.18 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 275 TYR 0.025 0.002 TYR A 243 PHE 0.011 0.001 PHE B 143 TRP 0.006 0.001 TRP B 436 HIS 0.007 0.001 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (12345) covalent geometry : angle 0.65490 / 0.32 (16833) hydrogen bonds : bond 0.04171 / 2.80 ( 590) hydrogen bonds : angle 4.62494 / 3.19 ( 1710) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.8693 (tpp) cc_final: 0.8458 (tpp) REVERT: B 166 MET cc_start: 0.9007 (mmm) cc_final: 0.8317 (mmm) REVERT: B 184 PHE cc_start: 0.6690 (t80) cc_final: 0.5868 (t80) REVERT: B 347 ASP cc_start: 0.7593 (p0) cc_final: 0.7238 (p0) REVERT: B 430 ASN cc_start: 0.8690 (t0) cc_final: 0.8449 (t0) REVERT: B 432 GLU cc_start: 0.9015 (mp0) cc_final: 0.8772 (mp0) REVERT: B 624 MET cc_start: 0.8388 (mmm) cc_final: 0.8134 (mmm) REVERT: B 792 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9005 (tptt) outliers start: 12 outliers final: 5 residues processed: 85 average time/residue: 0.1372 time to fit residues: 16.5865 Evaluate side-chains 81 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 792 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 110 optimal weight: 9.9990 chunk 68 optimal weight: 0.3980 chunk 142 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 471 HIS B 557 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.081174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.060415 restraints weight = 47782.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.061348 restraints weight = 26970.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.061354 restraints weight = 18965.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.061680 restraints weight = 20112.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.061703 restraints weight = 16845.390| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12345 Z= 0.123 Angle : 0.630 14.334 16833 Z= 0.310 Chirality : 0.041 0.291 1912 Planarity : 0.004 0.044 2104 Dihedral : 15.701 134.274 1940 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.74 % Allowed : 18.76 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.22), residues: 1456 helix: 1.23 (0.19), residues: 724 sheet: -0.66 (0.39), residues: 176 loop : -1.18 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.018 0.001 TYR A 243 PHE 0.013 0.001 PHE B 143 TRP 0.006 0.001 TRP B 436 HIS 0.004 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12345) covalent geometry : angle 0.63008 / 0.31 (16833) hydrogen bonds : bond 0.03909 / 2.62 ( 590) hydrogen bonds : angle 4.52521 / 3.12 ( 1710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1853.03 seconds wall clock time: 32 minutes 58.97 seconds (1978.97 seconds total)