Starting phenix.real_space_refine on Wed Mar 4 08:36:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ai7_11793/03_2026/7ai7_11793.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ai7_11793/03_2026/7ai7_11793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ai7_11793/03_2026/7ai7_11793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ai7_11793/03_2026/7ai7_11793.map" model { file = "/net/cci-nas-00/data/ceres_data/7ai7_11793/03_2026/7ai7_11793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ai7_11793/03_2026/7ai7_11793.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 53 5.16 5 C 7492 2.51 5 N 2160 2.21 5 O 2349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 2.72, 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: 1.10 Conformation dependent library (CDL) restraints added in 707.5 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: 1.60 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: 1.80 Time building geometry restraints manager: 1.46 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: 13308 2.46 - 4.92: 3229 4.92 - 7.38: 274 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: 973 0.070 - 0.140: 657 0.140 - 0.211: 212 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: 0.750 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.320 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: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 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= 1.126 Angle : 1.978 12.301 16833 Z= 1.446 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 covalent geometry : bond 0.01504 (12345) covalent geometry : angle 1.97751 (16833) hydrogen bonds : bond 0.23230 ( 590) hydrogen bonds : angle 9.59541 ( 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 : 0.480 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: 0.1342 time to fit residues: 33.3757 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 : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 694 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 557 ASN A 760 HIS B 216 GLN B 476 GLN B 526 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.084251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.062871 restraints weight = 47600.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.064470 restraints weight = 27392.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.065095 restraints weight = 17278.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.065338 restraints weight = 16496.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.065387 restraints weight = 13974.541| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12345 Z= 0.146 Angle : 0.664 9.209 16833 Z= 0.343 Chirality : 0.042 0.207 1912 Planarity : 0.004 0.042 2104 Dihedral : 16.616 168.277 1943 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.57 % Allowed : 13.64 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.62 (0.20), residues: 1456 helix: 0.59 (0.18), residues: 700 sheet: -1.36 (0.38), residues: 176 loop : -1.27 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 449 TYR 0.032 0.002 TYR A 509 PHE 0.018 0.002 PHE B 467 TRP 0.007 0.001 TRP B 137 HIS 0.003 0.001 HIS B 760 Details of bonding type rmsd covalent geometry : bond 0.00313 (12345) covalent geometry : angle 0.66357 (16833) hydrogen bonds : bond 0.05427 ( 590) hydrogen bonds : angle 5.39254 ( 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 132 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.459 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: A 13 MET cc_start: 0.7571 (ptt) cc_final: 0.7370 (ptt) REVERT: A 33 MET cc_start: 0.9038 (tpp) cc_final: 0.8755 (tpp) REVERT: A 364 ASP cc_start: 0.7982 (m-30) cc_final: 0.7732 (m-30) REVERT: A 430 ASN cc_start: 0.7214 (t0) cc_final: 0.6720 (t0) REVERT: B 166 MET cc_start: 0.8224 (mmm) cc_final: 0.7781 (mmm) REVERT: B 347 ASP cc_start: 0.7676 (p0) cc_final: 0.7176 (p0) REVERT: B 430 ASN cc_start: 0.8686 (t0) cc_final: 0.8271 (t0) REVERT: B 490 MET cc_start: 0.8633 (tmm) cc_final: 0.8379 (tmm) outliers start: 19 outliers final: 6 residues processed: 125 average time/residue: 0.1250 time to fit residues: 22.1771 Evaluate side-chains 88 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 414 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 25 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 96 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 626 GLN B 391 GLN B 590 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.082711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.061160 restraints weight = 48115.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.062480 restraints weight = 26889.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.063124 restraints weight = 18256.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.063281 restraints weight = 17308.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.063372 restraints weight = 15212.484| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12345 Z= 0.136 Angle : 0.618 12.761 16833 Z= 0.313 Chirality : 0.041 0.161 1912 Planarity : 0.004 0.047 2104 Dihedral : 16.138 156.687 1940 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.57 % Allowed : 16.45 % 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: -0.12 (0.21), residues: 1456 helix: 1.02 (0.19), residues: 706 sheet: -1.13 (0.37), residues: 186 loop : -1.06 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 163 TYR 0.033 0.002 TYR B 509 PHE 0.010 0.001 PHE B 467 TRP 0.007 0.001 TRP A 709 HIS 0.005 0.001 HIS B 760 Details of bonding type rmsd covalent geometry : bond 0.00295 (12345) covalent geometry : angle 0.61826 (16833) hydrogen bonds : bond 0.04500 ( 590) hydrogen bonds : angle 4.92284 ( 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 107 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.377 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: 0.9019 (tpp) cc_final: 0.8754 (tpp) REVERT: A 364 ASP cc_start: 0.7911 (m-30) cc_final: 0.7680 (m-30) REVERT: A 430 ASN cc_start: 0.7410 (t0) cc_final: 0.6807 (t0) REVERT: A 471 HIS cc_start: 0.8802 (m170) cc_final: 0.8588 (m170) REVERT: A 633 MET cc_start: 0.8258 (mtp) cc_final: 0.7992 (mtp) REVERT: A 775 VAL cc_start: 0.8301 (OUTLIER) cc_final: 0.8092 (p) REVERT: B 166 MET cc_start: 0.8625 (mmm) cc_final: 0.7993 (mmm) REVERT: B 347 ASP cc_start: 0.7526 (p0) cc_final: 0.7121 (p0) REVERT: B 430 ASN cc_start: 0.8664 (t0) cc_final: 0.8292 (t0) REVERT: B 490 MET cc_start: 0.8749 (tmm) cc_final: 0.8456 (tmm) outliers start: 19 outliers final: 10 residues processed: 100 average time/residue: 0.1166 time to fit residues: 16.6648 Evaluate side-chains 89 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 557 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 120 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.082427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.061077 restraints weight = 47516.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.062330 restraints weight = 25919.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.062813 restraints weight = 18185.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.063008 restraints weight = 16997.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.063100 restraints weight = 15087.515| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12345 Z= 0.126 Angle : 0.596 10.323 16833 Z= 0.299 Chirality : 0.040 0.160 1912 Planarity : 0.004 0.046 2104 Dihedral : 15.914 146.002 1940 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.74 % Allowed : 16.28 % 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: 0.12 (0.21), residues: 1456 helix: 1.21 (0.19), residues: 716 sheet: -0.72 (0.38), residues: 179 loop : -1.09 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 457 TYR 0.025 0.002 TYR B 509 PHE 0.008 0.001 PHE B 467 TRP 0.005 0.001 TRP A 709 HIS 0.008 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00276 (12345) covalent geometry : angle 0.59641 (16833) hydrogen bonds : bond 0.04081 ( 590) hydrogen bonds : angle 4.66751 ( 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: 21 poor density : 87 time to evaluate : 0.273 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: 0.8948 (tpp) cc_final: 0.8731 (tpp) REVERT: A 187 MET cc_start: 0.7968 (mmm) cc_final: 0.7610 (mmt) REVERT: A 364 ASP cc_start: 0.8039 (m-30) cc_final: 0.7813 (m-30) REVERT: A 471 HIS cc_start: 0.8758 (m170) cc_final: 0.8551 (m170) REVERT: A 535 LEU cc_start: 0.9036 (mp) cc_final: 0.8658 (tt) REVERT: B 166 MET cc_start: 0.8769 (mmm) cc_final: 0.8036 (mmm) REVERT: B 347 ASP cc_start: 0.7512 (p0) cc_final: 0.7144 (p0) REVERT: B 430 ASN cc_start: 0.8702 (t0) cc_final: 0.8365 (t0) REVERT: B 490 MET cc_start: 0.8813 (tmm) cc_final: 0.8571 (tmm) outliers start: 21 outliers final: 12 residues processed: 99 average time/residue: 0.1232 time to fit residues: 17.3349 Evaluate side-chains 91 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 727 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 69 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 21 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.078965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.057524 restraints weight = 48156.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.058369 restraints weight = 27411.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.059462 restraints weight = 19614.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.059315 restraints weight = 18475.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.059396 restraints weight = 16206.455| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12345 Z= 0.219 Angle : 0.685 9.660 16833 Z= 0.347 Chirality : 0.043 0.175 1912 Planarity : 0.005 0.047 2104 Dihedral : 15.988 146.254 1940 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.81 % Allowed : 15.79 % Favored : 81.40 % 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: -0.07 (0.21), residues: 1456 helix: 1.02 (0.19), residues: 716 sheet: -0.69 (0.39), residues: 171 loop : -1.17 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 491 TYR 0.027 0.002 TYR A 635 PHE 0.009 0.002 PHE B 725 TRP 0.009 0.001 TRP A 709 HIS 0.011 0.001 HIS B 760 Details of bonding type rmsd covalent geometry : bond 0.00492 (12345) covalent geometry : angle 0.68523 (16833) hydrogen bonds : bond 0.04747 ( 590) hydrogen bonds : angle 4.87277 ( 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 110 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 0.503 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: 0.8808 (tpp) cc_final: 0.8573 (tpp) REVERT: A 187 MET cc_start: 0.7779 (mmm) cc_final: 0.7380 (mmt) REVERT: A 364 ASP cc_start: 0.7967 (m-30) cc_final: 0.7763 (m-30) REVERT: A 790 ARG cc_start: 0.7169 (mmt180) cc_final: 0.6691 (mmt90) REVERT: B 166 MET cc_start: 0.9002 (mmm) cc_final: 0.8272 (mmm) REVERT: B 184 PHE cc_start: 0.6613 (t80) cc_final: 0.5869 (t80) REVERT: B 347 ASP cc_start: 0.7642 (p0) cc_final: 0.7257 (p0) REVERT: B 430 ASN cc_start: 0.8709 (t0) cc_final: 0.8403 (t0) REVERT: B 792 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.8899 (tppt) outliers start: 34 outliers final: 14 residues processed: 100 average time/residue: 0.1242 time to fit residues: 17.7027 Evaluate side-chains 86 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 792 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 91 optimal weight: 0.0270 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 114 optimal weight: 40.0000 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.079835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.058510 restraints weight = 48006.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.059458 restraints weight = 27147.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.059648 restraints weight = 20037.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.059938 restraints weight = 18465.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.059997 restraints weight = 16688.718| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12345 Z= 0.156 Angle : 0.626 12.378 16833 Z= 0.313 Chirality : 0.041 0.192 1912 Planarity : 0.004 0.047 2104 Dihedral : 15.859 143.885 1940 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.82 % Allowed : 17.36 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.22), residues: 1456 helix: 1.23 (0.19), residues: 714 sheet: -0.54 (0.40), residues: 171 loop : -1.13 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 457 TYR 0.019 0.002 TYR B 509 PHE 0.008 0.001 PHE A 155 TRP 0.008 0.001 TRP B 310 HIS 0.006 0.001 HIS B 760 Details of bonding type rmsd covalent geometry : bond 0.00352 (12345) covalent geometry : angle 0.62629 (16833) hydrogen bonds : bond 0.04140 ( 590) hydrogen bonds : angle 4.70743 ( 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 95 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.8718 (tpp) cc_final: 0.8446 (tpp) REVERT: A 364 ASP cc_start: 0.7993 (m-30) cc_final: 0.7769 (m-30) REVERT: B 166 MET cc_start: 0.9088 (mmm) cc_final: 0.8423 (mmm) REVERT: B 184 PHE cc_start: 0.6734 (t80) cc_final: 0.6060 (t80) REVERT: B 347 ASP cc_start: 0.7626 (p0) cc_final: 0.7245 (p0) REVERT: B 430 ASN cc_start: 0.8699 (t0) cc_final: 0.8118 (t0) REVERT: B 432 GLU cc_start: 0.9033 (mp0) cc_final: 0.8754 (mp0) REVERT: B 792 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.8994 (tptt) outliers start: 22 outliers final: 12 residues processed: 88 average time/residue: 0.1287 time to fit residues: 16.0501 Evaluate side-chains 83 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 187 MET 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 727 THR Chi-restraints excluded: chain B residue 792 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 113 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS B 557 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.079418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.057315 restraints weight = 48845.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.058621 restraints weight = 27921.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.059375 restraints weight = 18477.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.059636 restraints weight = 16937.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.059615 restraints weight = 14498.619| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4338 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= 0.124 Angle : 0.601 13.522 16833 Z= 0.296 Chirality : 0.040 0.221 1912 Planarity : 0.004 0.048 2104 Dihedral : 15.646 133.713 1940 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.65 % Allowed : 17.69 % 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: 0.26 (0.22), residues: 1456 helix: 1.37 (0.19), residues: 718 sheet: -0.52 (0.39), residues: 183 loop : -1.14 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 491 TYR 0.019 0.001 TYR B 509 PHE 0.013 0.001 PHE B 143 TRP 0.006 0.001 TRP A 137 HIS 0.005 0.001 HIS B 760 Details of bonding type rmsd covalent geometry : bond 0.00278 (12345) covalent geometry : angle 0.60065 (16833) hydrogen bonds : bond 0.03746 ( 590) hydrogen bonds : angle 4.51533 ( 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 95 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.8684 (tpp) cc_final: 0.8389 (tpp) REVERT: A 364 ASP cc_start: 0.7980 (m-30) cc_final: 0.7736 (m-30) REVERT: B 166 MET cc_start: 0.9128 (mmm) cc_final: 0.8409 (mmm) REVERT: B 347 ASP cc_start: 0.7561 (p0) cc_final: 0.7207 (p0) REVERT: B 432 GLU cc_start: 0.9068 (mp0) cc_final: 0.8809 (tp30) REVERT: B 792 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.8980 (tptt) outliers start: 20 outliers final: 14 residues processed: 89 average time/residue: 0.1222 time to fit residues: 15.3014 Evaluate side-chains 87 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 187 MET 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 467 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 68 optimal weight: 0.1980 chunk 10 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 471 HIS A 682 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.077948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.056607 restraints weight = 48221.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.057502 restraints weight = 29746.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.057467 restraints weight = 20948.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.057820 restraints weight = 20352.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.057906 restraints weight = 18410.274| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12345 Z= 0.255 Angle : 0.721 11.611 16833 Z= 0.360 Chirality : 0.044 0.178 1912 Planarity : 0.005 0.045 2104 Dihedral : 15.880 139.496 1940 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.74 % Allowed : 18.10 % Favored : 80.17 % 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: -0.13 (0.21), residues: 1456 helix: 1.04 (0.19), residues: 714 sheet: -0.68 (0.39), residues: 178 loop : -1.33 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 324 TYR 0.023 0.002 TYR A 635 PHE 0.015 0.002 PHE B 143 TRP 0.010 0.001 TRP B 709 HIS 0.020 0.002 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00575 (12345) covalent geometry : angle 0.72098 (16833) hydrogen bonds : bond 0.04614 ( 590) hydrogen bonds : angle 4.82739 ( 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 93 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.457 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: 0.7583 (ptt) cc_final: 0.7367 (mtm) REVERT: A 33 MET cc_start: 0.8567 (tpp) cc_final: 0.8304 (tpp) REVERT: A 364 ASP cc_start: 0.7925 (m-30) cc_final: 0.7705 (m-30) REVERT: B 166 MET cc_start: 0.9220 (mmm) cc_final: 0.8527 (mmm) REVERT: B 347 ASP cc_start: 0.7729 (p0) cc_final: 0.7334 (p0) REVERT: B 432 GLU cc_start: 0.9130 (mp0) cc_final: 0.8625 (tp30) REVERT: B 792 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.9011 (tppt) outliers start: 21 outliers final: 15 residues processed: 87 average time/residue: 0.1309 time to fit residues: 16.0234 Evaluate side-chains 85 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 792 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 58 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 47 optimal weight: 0.0470 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.079322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.057387 restraints weight = 48467.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.058699 restraints weight = 27378.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059226 restraints weight = 17983.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.059462 restraints weight = 17498.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.059501 restraints weight = 14747.235| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12345 Z= 0.121 Angle : 0.614 13.175 16833 Z= 0.303 Chirality : 0.040 0.175 1912 Planarity : 0.004 0.046 2104 Dihedral : 15.678 138.136 1940 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.07 % Allowed : 19.09 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.22), residues: 1456 helix: 1.46 (0.19), residues: 703 sheet: -0.56 (0.39), residues: 183 loop : -1.13 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 449 TYR 0.017 0.001 TYR B 509 PHE 0.021 0.001 PHE B 143 TRP 0.009 0.001 TRP A 137 HIS 0.004 0.001 HIS B 760 Details of bonding type rmsd covalent geometry : bond 0.00266 (12345) covalent geometry : angle 0.61394 (16833) hydrogen bonds : bond 0.03690 ( 590) hydrogen bonds : angle 4.52297 ( 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 85 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.303 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 364 ASP cc_start: 0.7955 (m-30) cc_final: 0.7690 (m-30) REVERT: B 166 MET cc_start: 0.9253 (mmm) cc_final: 0.8618 (mmm) REVERT: B 347 ASP cc_start: 0.7600 (p0) cc_final: 0.7254 (p0) REVERT: B 432 GLU cc_start: 0.9107 (mp0) cc_final: 0.8628 (tp30) REVERT: B 792 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8978 (tptt) outliers start: 13 outliers final: 9 residues processed: 81 average time/residue: 0.1311 time to fit residues: 14.8620 Evaluate side-chains 78 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 792 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 103 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 0.0670 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.079767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.057781 restraints weight = 48529.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.059100 restraints weight = 27230.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.059585 restraints weight = 18204.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.059893 restraints weight = 16904.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.059937 restraints weight = 14908.252| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12345 Z= 0.120 Angle : 0.623 15.090 16833 Z= 0.303 Chirality : 0.040 0.173 1912 Planarity : 0.004 0.050 2104 Dihedral : 15.494 135.914 1940 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.91 % Allowed : 19.34 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.34 (0.22), residues: 1456 helix: 1.54 (0.20), residues: 705 sheet: -0.55 (0.39), residues: 181 loop : -1.17 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 491 TYR 0.038 0.002 TYR A 243 PHE 0.020 0.001 PHE B 143 TRP 0.008 0.001 TRP A 137 HIS 0.003 0.000 HIS B 760 Details of bonding type rmsd covalent geometry : bond 0.00268 (12345) covalent geometry : angle 0.62281 (16833) hydrogen bonds : bond 0.03603 ( 590) hydrogen bonds : angle 4.44663 ( 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 83 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.437 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: 0.7230 (mtm) cc_final: 0.6840 (mpp) REVERT: A 364 ASP cc_start: 0.7902 (m-30) cc_final: 0.7638 (m-30) REVERT: B 166 MET cc_start: 0.9240 (mmm) cc_final: 0.8553 (mmm) REVERT: B 347 ASP cc_start: 0.7535 (p0) cc_final: 0.7216 (p0) REVERT: B 432 GLU cc_start: 0.9111 (mp0) cc_final: 0.8674 (tp30) REVERT: B 792 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9005 (tptt) outliers start: 11 outliers final: 7 residues processed: 81 average time/residue: 0.1209 time to fit residues: 14.1135 Evaluate side-chains 78 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 792 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 110 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 109 optimal weight: 0.0770 chunk 77 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 115 optimal weight: 0.0470 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.080568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.059019 restraints weight = 47835.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.060737 restraints weight = 26259.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.061193 restraints weight = 16264.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.061410 restraints weight = 16150.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.061482 restraints weight = 13637.193| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12345 Z= 0.113 Angle : 0.603 13.737 16833 Z= 0.294 Chirality : 0.040 0.175 1912 Planarity : 0.004 0.049 2104 Dihedral : 15.400 135.584 1940 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.99 % Allowed : 19.59 % Favored : 79.42 % 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: 0.42 (0.22), residues: 1456 helix: 1.60 (0.20), residues: 705 sheet: -0.54 (0.37), residues: 198 loop : -1.13 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 491 TYR 0.018 0.001 TYR B 509 PHE 0.021 0.001 PHE B 143 TRP 0.009 0.001 TRP A 137 HIS 0.002 0.000 HIS A 728 Details of bonding type rmsd covalent geometry : bond 0.00251 (12345) covalent geometry : angle 0.60300 (16833) hydrogen bonds : bond 0.03457 ( 590) hydrogen bonds : angle 4.34962 ( 1710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1747.12 seconds wall clock time: 30 minutes 58.51 seconds (1858.51 seconds total)