Starting phenix.real_space_refine on Sat Oct 24 03:48:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ai7_11793/10_2026/7ai7_11793.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ai7_11793/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ai7_11793/10_2026/7ai7_11793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ai7_11793/10_2026/7ai7_11793.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ai7_11793/10_2026/7ai7_11793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ai7_11793/10_2026/7ai7_11793.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ai7_11793/10_2026/7ai7_11793.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ai7_11793/10_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-2.3rc1-6221/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: 2.80, per 1000 atoms: 0.23 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: 0.99 Conformation dependent library (CDL) restraints added in 611.1 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: 1.52 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: 2.14 Time building geometry restraints manager: 1.33 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.440 Find NCS groups from input model: 0.040 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.340 ------------------------------------------------------------------------------- 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 1.97226 / 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 : 0.453 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: 0.1242 time to fit residues: 31.2747 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 : 0.435 ------------------------------------------------------------------------------- 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: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] 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 B 526 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.084090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.062889 restraints weight = 47405.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.064626 restraints weight = 27169.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.065890 restraints weight = 16962.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.065840 restraints weight = 15551.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.065818 restraints weight = 12715.782| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12345 Z= 0.172 Angle : 0.729 11.103 16833 Z= 0.380 Chirality : 0.044 0.263 1912 Planarity : 0.005 0.044 2104 Dihedral : 16.881 166.591 1943 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.49 % Allowed : 13.88 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.84 (0.20), residues: 1456 helix: 0.38 (0.18), residues: 698 sheet: -1.47 (0.37), residues: 192 loop : -1.30 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 652 TYR 0.025 0.002 TYR A 473 PHE 0.015 0.002 PHE B 467 TRP 0.008 0.001 TRP B 202 HIS 0.005 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (12345) covalent geometry : angle 0.72946 / 0.38 (16833) hydrogen bonds : bond 0.06224 / 4.15 ( 590) hydrogen bonds : angle 5.73651 / 3.91 ( 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: 18 poor density : 107 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.7543 (ptt) cc_final: 0.7180 (ppp) REVERT: A 33 MET cc_start: 0.8903 (tpp) cc_final: 0.8631 (tpp) REVERT: A 165 THR cc_start: 0.7748 (m) cc_final: 0.7534 (p) REVERT: A 361 ARG cc_start: 0.6600 (mtt180) cc_final: 0.6347 (mtt180) REVERT: A 430 ASN cc_start: 0.7243 (t0) cc_final: 0.6709 (t0) REVERT: B 166 MET cc_start: 0.8141 (mmm) cc_final: 0.7754 (mmm) REVERT: B 184 PHE cc_start: 0.6220 (t80) cc_final: 0.5266 (t80) REVERT: B 306 MET cc_start: 0.7581 (tpp) cc_final: 0.7359 (tpp) REVERT: B 347 ASP cc_start: 0.7793 (p0) cc_final: 0.7256 (p0) REVERT: B 430 ASN cc_start: 0.8611 (t0) cc_final: 0.8245 (t0) REVERT: B 432 GLU cc_start: 0.8988 (mp0) cc_final: 0.8787 (mp0) REVERT: B 490 MET cc_start: 0.8513 (tmm) cc_final: 0.8283 (tmm) outliers start: 18 outliers final: 4 residues processed: 116 average time/residue: 0.1096 time to fit residues: 18.0649 Evaluate side-chains 90 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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: [25, 69, 4, 101, 74, 95, 103, 47, 92, 96, 31] chunk 25 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 590 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.082531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.061172 restraints weight = 47899.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.062531 restraints weight = 26534.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.063219 restraints weight = 17745.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.063514 restraints weight = 16504.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.063521 restraints weight = 14155.903| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2714 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= 0.159 Angle : 0.667 12.172 16833 Z= 0.341 Chirality : 0.043 0.255 1912 Planarity : 0.005 0.048 2104 Dihedral : 16.558 165.163 1940 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.49 % Allowed : 16.53 % Favored : 81.98 % 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: -0.40 (0.21), residues: 1456 helix: 0.73 (0.19), residues: 700 sheet: -1.00 (0.38), residues: 181 loop : -1.18 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 652 TYR 0.026 0.002 TYR A 473 PHE 0.011 0.001 PHE B 467 TRP 0.005 0.001 TRP B 137 HIS 0.005 0.001 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (12345) covalent geometry : angle 0.66726 / 0.34 (16833) hydrogen bonds : bond 0.05405 / 3.59 ( 590) hydrogen bonds : angle 5.26826 / 3.61 ( 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 105 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.330 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: A 13 MET cc_start: 0.7553 (ptt) cc_final: 0.7317 (ppp) REVERT: A 33 MET cc_start: 0.9044 (tpp) cc_final: 0.8691 (tpp) REVERT: A 187 MET cc_start: 0.7888 (mmm) cc_final: 0.7512 (mmt) REVERT: A 430 ASN cc_start: 0.7277 (t0) cc_final: 0.6868 (t0) REVERT: A 633 MET cc_start: 0.8272 (mtp) cc_final: 0.7990 (mtp) REVERT: A 671 MET cc_start: 0.7744 (tpp) cc_final: 0.7472 (tpp) REVERT: B 166 MET cc_start: 0.8335 (mmm) cc_final: 0.7862 (mmm) REVERT: B 347 ASP cc_start: 0.7731 (p0) cc_final: 0.7285 (p0) REVERT: B 430 ASN cc_start: 0.8748 (t0) cc_final: 0.8486 (t0) REVERT: B 490 MET cc_start: 0.8603 (tmm) cc_final: 0.8372 (tmm) outliers start: 18 outliers final: 9 residues processed: 99 average time/residue: 0.1183 time to fit residues: 16.8960 Evaluate side-chains 84 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 557 ASN 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: [120, 1, 134, 42, 106, 81, 43, 28, 69, 75, 126] chunk 120 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.080011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.058307 restraints weight = 48020.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.059603 restraints weight = 26537.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.059836 restraints weight = 19101.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.059997 restraints weight = 18143.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.060072 restraints weight = 16419.825| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12345 Z= 0.213 Angle : 0.696 7.837 16833 Z= 0.355 Chirality : 0.044 0.226 1912 Planarity : 0.005 0.048 2104 Dihedral : 16.355 156.235 1940 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.07 % Allowed : 16.86 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.37 (0.21), residues: 1456 helix: 0.73 (0.18), residues: 709 sheet: -0.79 (0.43), residues: 144 loop : -1.23 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 163 TYR 0.039 0.002 TYR B 509 PHE 0.011 0.002 PHE B 654 TRP 0.011 0.001 TRP B 436 HIS 0.010 0.001 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (12345) covalent geometry : angle 0.69555 / 0.36 (16833) hydrogen bonds : bond 0.05179 / 3.45 ( 590) hydrogen bonds : angle 5.11888 / 3.52 ( 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 108 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.297 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 13 MET cc_start: 0.7619 (ptt) cc_final: 0.7254 (ppp) REVERT: A 33 MET cc_start: 0.9078 (tpp) cc_final: 0.8759 (tpp) REVERT: A 430 ASN cc_start: 0.7229 (t0) cc_final: 0.7005 (t0) REVERT: A 471 HIS cc_start: 0.8884 (m170) cc_final: 0.8556 (m170) REVERT: A 535 LEU cc_start: 0.9175 (mp) cc_final: 0.8765 (tt) REVERT: A 775 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8244 (p) REVERT: B 166 MET cc_start: 0.8704 (mmm) cc_final: 0.8079 (mmm) REVERT: B 187 MET cc_start: 0.8634 (mmm) cc_final: 0.8158 (mmp) REVERT: B 347 ASP cc_start: 0.7691 (p0) cc_final: 0.7224 (p0) REVERT: B 368 MET cc_start: 0.8601 (mtp) cc_final: 0.8356 (ptp) REVERT: B 430 ASN cc_start: 0.8813 (t0) cc_final: 0.8426 (t0) REVERT: B 432 GLU cc_start: 0.9130 (mp0) cc_final: 0.8922 (mp0) REVERT: B 490 MET cc_start: 0.8729 (tmm) cc_final: 0.8490 (tmm) outliers start: 25 outliers final: 12 residues processed: 101 average time/residue: 0.1080 time to fit residues: 15.6644 Evaluate side-chains 93 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain B residue 143 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 414 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 557 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: [69, 48, 122, 103, 21, 90, 47, 141, 30, 10, 128] chunk 69 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN A 599 ASN B 339 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.079137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.057742 restraints weight = 48379.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058771 restraints weight = 27448.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.059001 restraints weight = 20837.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.059417 restraints weight = 19867.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.059377 restraints weight = 16839.281| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12345 Z= 0.214 Angle : 0.682 9.300 16833 Z= 0.349 Chirality : 0.044 0.182 1912 Planarity : 0.005 0.051 2104 Dihedral : 16.255 153.934 1940 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.56 % Allowed : 16.78 % Favored : 80.66 % 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: -0.32 (0.21), residues: 1456 helix: 0.81 (0.19), residues: 710 sheet: -0.74 (0.43), residues: 144 loop : -1.29 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 790 TYR 0.023 0.002 TYR A 635 PHE 0.012 0.002 PHE A 467 TRP 0.007 0.001 TRP B 436 HIS 0.008 0.001 HIS A 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (12345) covalent geometry : angle 0.68175 / 0.35 (16833) hydrogen bonds : bond 0.05042 / 3.37 ( 590) hydrogen bonds : angle 5.00275 / 3.46 ( 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 115 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.355 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: 0.7777 (ptt) cc_final: 0.7260 (ppp) REVERT: A 33 MET cc_start: 0.8929 (tpp) cc_final: 0.8601 (tpp) REVERT: A 471 HIS cc_start: 0.8829 (m170) cc_final: 0.8601 (m170) REVERT: A 535 LEU cc_start: 0.9126 (mp) cc_final: 0.8720 (tt) REVERT: A 633 MET cc_start: 0.8426 (mtp) cc_final: 0.8080 (mtp) REVERT: A 705 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8767 (tt) REVERT: A 775 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8259 (p) REVERT: B 166 MET cc_start: 0.8846 (mmm) cc_final: 0.8186 (mmm) REVERT: B 347 ASP cc_start: 0.7760 (p0) cc_final: 0.7307 (p0) REVERT: B 490 MET cc_start: 0.8729 (tmm) cc_final: 0.8519 (tmm) REVERT: B 653 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8541 (mt) outliers start: 31 outliers final: 17 residues processed: 107 average time/residue: 0.1141 time to fit residues: 17.3779 Evaluate side-chains 98 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 775 VAL 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 414 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 653 ILE 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: [91, 16, 100, 114, 30, 29, 6, 38, 126, 81, 97] chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.079834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.058101 restraints weight = 48229.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.059459 restraints weight = 26884.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.059933 restraints weight = 18472.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.060067 restraints weight = 18013.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.060124 restraints weight = 15872.201| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3709 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= 0.155 Angle : 0.645 12.666 16833 Z= 0.324 Chirality : 0.043 0.311 1912 Planarity : 0.004 0.046 2104 Dihedral : 16.127 149.928 1940 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.98 % Allowed : 17.60 % 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: -0.18 (0.21), residues: 1456 helix: 0.93 (0.19), residues: 712 sheet: -0.64 (0.41), residues: 156 loop : -1.25 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.018 0.002 TYR B 635 PHE 0.008 0.001 PHE B 532 TRP 0.007 0.001 TRP B 709 HIS 0.005 0.001 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (12345) covalent geometry : angle 0.64453 / 0.32 (16833) hydrogen bonds : bond 0.04608 / 3.05 ( 590) hydrogen bonds : angle 4.88631 / 3.36 ( 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 105 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.284 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: 0.7760 (ptt) cc_final: 0.7217 (ppp) REVERT: A 33 MET cc_start: 0.8890 (tpp) cc_final: 0.8592 (tpp) REVERT: A 471 HIS cc_start: 0.8867 (m170) cc_final: 0.8658 (m170) REVERT: A 535 LEU cc_start: 0.9117 (mp) cc_final: 0.8690 (tt) REVERT: A 633 MET cc_start: 0.8326 (mtp) cc_final: 0.7964 (mtp) REVERT: B 166 MET cc_start: 0.8900 (mmm) cc_final: 0.8129 (mmm) REVERT: B 347 ASP cc_start: 0.7641 (p0) cc_final: 0.7237 (p0) REVERT: B 368 MET cc_start: 0.8728 (mtp) cc_final: 0.8453 (ptp) REVERT: B 432 GLU cc_start: 0.9089 (mp0) cc_final: 0.8695 (mp0) REVERT: B 490 MET cc_start: 0.8782 (tmm) cc_final: 0.8533 (tmm) outliers start: 24 outliers final: 14 residues processed: 95 average time/residue: 0.1304 time to fit residues: 17.3212 Evaluate side-chains 89 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 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 302 MET 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 Chi-restraints excluded: chain B residue 735 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: [113, 63, 120, 30, 51, 119, 112, 20, 109, 7, 53] chunk 113 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.080222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.057806 restraints weight = 48331.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.059446 restraints weight = 27509.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.060495 restraints weight = 19229.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.061062 restraints weight = 15472.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.061541 restraints weight = 13704.055| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12345 Z= 0.138 Angle : 0.630 11.895 16833 Z= 0.315 Chirality : 0.042 0.178 1912 Planarity : 0.004 0.047 2104 Dihedral : 15.969 145.640 1940 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.90 % Allowed : 18.43 % Favored : 79.67 % 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 (0.21), residues: 1456 helix: 0.98 (0.19), residues: 717 sheet: -0.69 (0.38), residues: 192 loop : -1.23 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 449 TYR 0.016 0.001 TYR B 635 PHE 0.009 0.001 PHE A 467 TRP 0.006 0.001 TRP B 436 HIS 0.004 0.001 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (12345) covalent geometry : angle 0.62968 / 0.32 (16833) hydrogen bonds : bond 0.04385 / 2.93 ( 590) hydrogen bonds : angle 4.79279 / 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: 23 poor density : 79 time to evaluate : 0.386 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 13 MET cc_start: 0.7749 (ptt) cc_final: 0.7254 (ppp) REVERT: A 33 MET cc_start: 0.8859 (tpp) cc_final: 0.8507 (tpp) REVERT: A 471 HIS cc_start: 0.8821 (m170) cc_final: 0.8612 (m170) REVERT: A 633 MET cc_start: 0.8316 (mtp) cc_final: 0.7927 (mtp) REVERT: A 790 ARG cc_start: 0.7230 (mpt180) cc_final: 0.6284 (mmt180) REVERT: B 166 MET cc_start: 0.8887 (mmm) cc_final: 0.8170 (mmm) REVERT: B 184 PHE cc_start: 0.6419 (t80) cc_final: 0.5722 (t80) REVERT: B 347 ASP cc_start: 0.7590 (p0) cc_final: 0.7182 (p0) REVERT: B 368 MET cc_start: 0.8671 (mtp) cc_final: 0.8410 (ptp) REVERT: B 432 GLU cc_start: 0.8965 (mp0) cc_final: 0.8559 (mp0) REVERT: B 490 MET cc_start: 0.8762 (tmm) cc_final: 0.8557 (tmm) outliers start: 23 outliers final: 11 residues processed: 93 average time/residue: 0.1104 time to fit residues: 14.6448 Evaluate side-chains 87 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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 414 THR 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: [39, 82, 20, 57, 68, 10, 137, 43, 118, 71, 17] chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 0.0040 chunk 137 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 17 optimal weight: 30.0000 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.079268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.056794 restraints weight = 48053.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.058401 restraints weight = 27435.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.059436 restraints weight = 19156.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.060084 restraints weight = 15448.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.060463 restraints weight = 13607.974| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12345 Z= 0.184 Angle : 0.664 12.965 16833 Z= 0.331 Chirality : 0.043 0.163 1912 Planarity : 0.004 0.047 2104 Dihedral : 15.947 144.796 1940 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.74 % Allowed : 18.35 % Favored : 79.92 % 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: -0.19 (0.21), residues: 1456 helix: 0.94 (0.19), residues: 717 sheet: -0.65 (0.39), residues: 181 loop : -1.30 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 790 TYR 0.019 0.002 TYR A 635 PHE 0.008 0.001 PHE B 143 TRP 0.006 0.001 TRP B 709 HIS 0.007 0.001 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (12345) covalent geometry : angle 0.66357 / 0.33 (16833) hydrogen bonds : bond 0.04488 / 2.99 ( 590) hydrogen bonds : angle 4.79914 / 3.30 ( 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 99 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.439 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 13 MET cc_start: 0.7717 (ptt) cc_final: 0.7249 (ppp) REVERT: A 33 MET cc_start: 0.8779 (tpp) cc_final: 0.8461 (tpp) REVERT: A 471 HIS cc_start: 0.8814 (m170) cc_final: 0.8602 (m170) REVERT: A 633 MET cc_start: 0.8371 (mtp) cc_final: 0.8037 (mtp) REVERT: B 166 MET cc_start: 0.8992 (mmm) cc_final: 0.8297 (mmm) REVERT: B 184 PHE cc_start: 0.6521 (t80) cc_final: 0.5797 (t80) REVERT: B 347 ASP cc_start: 0.7660 (p0) cc_final: 0.7277 (p0) REVERT: B 432 GLU cc_start: 0.8937 (mp0) cc_final: 0.8534 (mp0) outliers start: 21 outliers final: 13 residues processed: 91 average time/residue: 0.1190 time to fit residues: 15.4573 Evaluate side-chains 89 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 685 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 414 THR Chi-restraints excluded: chain B residue 573 ILE 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: [58, 130, 38, 56, 107, 2, 61, 52, 47, 31, 72] chunk 58 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 557 ASN 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 = 0.080164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.058596 restraints weight = 47917.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.060031 restraints weight = 27717.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.060254 restraints weight = 19022.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.060477 restraints weight = 18005.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.060534 restraints weight = 16117.327| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12345 Z= 0.134 Angle : 0.646 13.930 16833 Z= 0.319 Chirality : 0.042 0.343 1912 Planarity : 0.004 0.045 2104 Dihedral : 15.868 142.443 1940 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.07 % Allowed : 18.93 % Favored : 80.00 % 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: -0.08 (0.21), residues: 1456 helix: 1.06 (0.19), residues: 718 sheet: -0.70 (0.39), residues: 183 loop : -1.26 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 275 TYR 0.018 0.001 TYR B 635 PHE 0.015 0.001 PHE B 143 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 0.00293 / 0.13 (12345) covalent geometry : angle 0.64575 / 0.32 (16833) hydrogen bonds : bond 0.04179 / 2.80 ( 590) hydrogen bonds : angle 4.70826 / 3.23 ( 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 95 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.396 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 13 MET cc_start: 0.7777 (ptt) cc_final: 0.7295 (ppp) REVERT: A 33 MET cc_start: 0.8669 (tpp) cc_final: 0.8402 (tpp) REVERT: A 471 HIS cc_start: 0.8813 (m170) cc_final: 0.8578 (m170) REVERT: A 633 MET cc_start: 0.8243 (mtp) cc_final: 0.7852 (mtp) REVERT: B 166 MET cc_start: 0.9063 (mmm) cc_final: 0.8281 (mmm) REVERT: B 184 PHE cc_start: 0.6886 (t80) cc_final: 0.6120 (t80) REVERT: B 347 ASP cc_start: 0.7647 (p0) cc_final: 0.7249 (p0) REVERT: B 432 GLU cc_start: 0.9048 (mp0) cc_final: 0.8631 (mp0) outliers start: 13 outliers final: 9 residues processed: 90 average time/residue: 0.1231 time to fit residues: 15.7161 Evaluate side-chains 86 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 467 PHE 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 573 ILE Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 727 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: [103, 67, 69, 75, 39, 30, 54, 110, 24, 56, 102] chunk 103 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 75 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 24 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 476 GLN B 557 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.081077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.058990 restraints weight = 47761.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.060655 restraints weight = 26843.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.061734 restraints weight = 18586.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.062374 restraints weight = 14861.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.062794 restraints weight = 13052.953| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12345 Z= 0.122 Angle : 0.635 13.992 16833 Z= 0.314 Chirality : 0.042 0.259 1912 Planarity : 0.004 0.047 2104 Dihedral : 15.747 136.491 1940 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.32 % Allowed : 18.60 % Favored : 80.08 % 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 (0.22), residues: 1456 helix: 1.13 (0.19), residues: 724 sheet: -0.56 (0.39), residues: 174 loop : -1.23 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 275 TYR 0.016 0.001 TYR B 473 PHE 0.019 0.001 PHE A 670 TRP 0.007 0.001 TRP A 137 HIS 0.004 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (12345) covalent geometry : angle 0.63458 / 0.31 (16833) hydrogen bonds : bond 0.04005 / 2.67 ( 590) hydrogen bonds : angle 4.62159 / 3.17 ( 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 99 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.411 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: A 33 MET cc_start: 0.8650 (tpp) cc_final: 0.8341 (tpp) REVERT: A 187 MET cc_start: 0.7685 (mmm) cc_final: 0.7180 (mmt) REVERT: A 633 MET cc_start: 0.8116 (mtp) cc_final: 0.7751 (mtp) REVERT: B 166 MET cc_start: 0.9007 (mmm) cc_final: 0.8255 (mmm) REVERT: B 184 PHE cc_start: 0.6526 (t80) cc_final: 0.5823 (t80) REVERT: B 347 ASP cc_start: 0.7485 (p0) cc_final: 0.7099 (p0) REVERT: B 432 GLU cc_start: 0.8856 (mp0) cc_final: 0.8412 (mp0) REVERT: B 792 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8848 (tptt) outliers start: 16 outliers final: 9 residues processed: 94 average time/residue: 0.1152 time to fit residues: 15.3637 Evaluate side-chains 87 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 269 MET Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 727 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: [110, 68, 142, 61, 7, 120, 105, 109, 77, 87, 115] chunk 110 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 142 optimal weight: 0.0010 chunk 61 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 115 optimal weight: 30.0000 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 476 GLN B 557 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.080671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.059190 restraints weight = 47983.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.060706 restraints weight = 28077.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.061510 restraints weight = 18126.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.061690 restraints weight = 17888.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.061677 restraints weight = 14533.368| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4335 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= 0.140 Angle : 0.658 13.933 16833 Z= 0.327 Chirality : 0.043 0.240 1912 Planarity : 0.004 0.063 2104 Dihedral : 15.734 135.342 1940 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.40 % Allowed : 18.93 % Favored : 79.67 % 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: -0.00 (0.21), residues: 1456 helix: 1.12 (0.19), residues: 720 sheet: -0.58 (0.40), residues: 168 loop : -1.25 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 163 TYR 0.051 0.002 TYR A 243 PHE 0.017 0.001 PHE B 143 TRP 0.006 0.001 TRP A 137 HIS 0.006 0.001 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (12345) covalent geometry : angle 0.65850 / 0.33 (16833) hydrogen bonds : bond 0.04067 / 2.71 ( 590) hydrogen bonds : angle 4.64816 / 3.19 ( 1710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1784.41 seconds wall clock time: 31 minutes 37.86 seconds (1897.86 seconds total)