Starting phenix.real_space_refine on Wed Jul 30 09:27:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ai7_11793/07_2025/7ai7_11793.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ai7_11793/07_2025/7ai7_11793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ai7_11793/07_2025/7ai7_11793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ai7_11793/07_2025/7ai7_11793.map" model { file = "/net/cci-nas-00/data/ceres_data/7ai7_11793/07_2025/7ai7_11793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ai7_11793/07_2025/7ai7_11793.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.42, per 1000 atoms: 0.61 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: 2.91 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 3.93 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: 4.04 Time building geometry restraints manager: 3.44 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: 0.880 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 32.510 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.210 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (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 TRP 0.055 0.007 TRP A 137 HIS 0.025 0.005 HIS A 752 PHE 0.054 0.006 PHE A 204 TYR 0.039 0.005 TYR A 623 ARG 0.036 0.002 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.23230 ( 590) hydrogen bonds : angle 9.59541 ( 1710) covalent geometry : bond 0.01504 (12345) covalent geometry : angle 1.97751 (16833) *********************** 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 : 1.499 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: 0.3544 time to fit residues: 88.1601 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 : 1.371 ------------------------------------------------------------------------------- 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 124 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.083237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.061891 restraints weight = 47435.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.063344 restraints weight = 26354.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.064721 restraints weight = 17371.816| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2456 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= 0.161 Angle : 0.675 10.038 16833 Z= 0.348 Chirality : 0.042 0.204 1912 Planarity : 0.004 0.044 2104 Dihedral : 16.645 165.655 1943 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.49 % Allowed : 13.97 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.20), residues: 1456 helix: 0.60 (0.18), residues: 699 sheet: -1.29 (0.38), residues: 174 loop : -1.26 (0.23), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 137 HIS 0.005 0.001 HIS B 760 PHE 0.019 0.002 PHE B 467 TYR 0.029 0.002 TYR A 509 ARG 0.008 0.000 ARG B 449 Details of bonding type rmsd hydrogen bonds : bond 0.05468 ( 590) hydrogen bonds : angle 5.42390 ( 1710) covalent geometry : bond 0.00344 (12345) covalent geometry : angle 0.67453 (16833) *********************** 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 128 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.422 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 33 MET cc_start: 0.9075 (tpp) cc_final: 0.8781 (tpp) REVERT: A 430 ASN cc_start: 0.6995 (t0) cc_final: 0.6561 (t0) REVERT: A 692 MET cc_start: 0.7947 (mtt) cc_final: 0.7692 (mtp) REVERT: A 790 ARG cc_start: 0.7261 (mmt180) cc_final: 0.7040 (mmt90) REVERT: B 166 MET cc_start: 0.8245 (mmm) cc_final: 0.7806 (mmm) REVERT: B 347 ASP cc_start: 0.7755 (p0) cc_final: 0.7243 (p0) REVERT: B 430 ASN cc_start: 0.8658 (t0) cc_final: 0.8281 (t0) REVERT: B 490 MET cc_start: 0.8591 (tmm) cc_final: 0.8340 (tmm) outliers start: 18 outliers final: 6 residues processed: 121 average time/residue: 0.2900 time to fit residues: 49.6323 Evaluate side-chains 85 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 36 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.082883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.061441 restraints weight = 48061.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.062764 restraints weight = 26444.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.063541 restraints weight = 17808.726| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12345 Z= 0.131 Angle : 0.623 12.242 16833 Z= 0.315 Chirality : 0.041 0.188 1912 Planarity : 0.004 0.047 2104 Dihedral : 16.185 156.637 1940 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.65 % Allowed : 16.20 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.21), residues: 1456 helix: 1.02 (0.19), residues: 710 sheet: -1.12 (0.36), residues: 192 loop : -1.12 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 137 HIS 0.004 0.001 HIS B 760 PHE 0.011 0.001 PHE B 467 TYR 0.030 0.002 TYR B 509 ARG 0.011 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 590) hydrogen bonds : angle 4.93733 ( 1710) covalent geometry : bond 0.00281 (12345) covalent geometry : angle 0.62327 (16833) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.9014 (tpp) cc_final: 0.8751 (tpp) REVERT: A 364 ASP cc_start: 0.7909 (m-30) cc_final: 0.7687 (m-30) REVERT: A 430 ASN cc_start: 0.7293 (t0) cc_final: 0.6707 (t0) REVERT: A 471 HIS cc_start: 0.8758 (m170) cc_final: 0.8482 (m170) REVERT: A 739 MET cc_start: 0.7787 (ttt) cc_final: 0.7480 (ttm) REVERT: A 775 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.8020 (p) REVERT: A 790 ARG cc_start: 0.7233 (mmt180) cc_final: 0.6888 (mmt90) REVERT: B 166 MET cc_start: 0.8609 (mmm) cc_final: 0.8007 (mmm) REVERT: B 347 ASP cc_start: 0.7543 (p0) cc_final: 0.7137 (p0) REVERT: B 430 ASN cc_start: 0.8747 (t0) cc_final: 0.8335 (t0) REVERT: B 490 MET cc_start: 0.8763 (tmm) cc_final: 0.8518 (tmm) outliers start: 20 outliers final: 8 residues processed: 104 average time/residue: 0.2770 time to fit residues: 42.1852 Evaluate side-chains 85 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 775 VAL 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 556 VAL 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 8 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.082310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.060816 restraints weight = 47593.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.061988 restraints weight = 26214.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.062719 restraints weight = 18690.352| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12345 Z= 0.126 Angle : 0.592 9.550 16833 Z= 0.299 Chirality : 0.040 0.160 1912 Planarity : 0.004 0.053 2104 Dihedral : 15.889 143.405 1940 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.98 % Allowed : 16.28 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1456 helix: 1.20 (0.19), residues: 717 sheet: -0.82 (0.37), residues: 196 loop : -0.99 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS B 760 PHE 0.017 0.001 PHE A 184 TYR 0.018 0.001 TYR A 501 ARG 0.006 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 590) hydrogen bonds : angle 4.70167 ( 1710) covalent geometry : bond 0.00274 (12345) covalent geometry : angle 0.59165 (16833) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 1.445 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 33 MET cc_start: 0.8969 (tpp) cc_final: 0.8718 (tpp) REVERT: A 467 PHE cc_start: 0.7529 (p90) cc_final: 0.7219 (p90) REVERT: A 471 HIS cc_start: 0.8693 (m170) cc_final: 0.8488 (m170) REVERT: A 490 MET cc_start: 0.7251 (tmm) cc_final: 0.6960 (tmm) REVERT: A 501 TYR cc_start: 0.7632 (m-10) cc_final: 0.7361 (m-10) REVERT: A 535 LEU cc_start: 0.9050 (mp) cc_final: 0.8663 (tt) REVERT: A 775 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.8040 (p) REVERT: A 790 ARG cc_start: 0.7227 (mmt180) cc_final: 0.6860 (mmt90) REVERT: B 166 MET cc_start: 0.8807 (mmm) cc_final: 0.8051 (mmm) REVERT: B 347 ASP cc_start: 0.7531 (p0) cc_final: 0.7168 (p0) REVERT: B 430 ASN cc_start: 0.8726 (t0) cc_final: 0.8440 (t0) outliers start: 24 outliers final: 11 residues processed: 103 average time/residue: 0.2737 time to fit residues: 40.6094 Evaluate side-chains 90 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 775 VAL 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 556 VAL 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: 2.9990 chunk 121 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 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 = 0.3793 r_free = 0.3793 target = 0.079494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.058172 restraints weight = 47452.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.059253 restraints weight = 25816.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.059633 restraints weight = 18824.884| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3953 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= 0.197 Angle : 0.654 10.828 16833 Z= 0.330 Chirality : 0.042 0.163 1912 Planarity : 0.005 0.048 2104 Dihedral : 15.900 142.487 1940 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.73 % Allowed : 16.36 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1456 helix: 1.12 (0.19), residues: 720 sheet: -0.64 (0.40), residues: 171 loop : -1.14 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 709 HIS 0.009 0.001 HIS B 760 PHE 0.009 0.002 PHE B 467 TYR 0.024 0.002 TYR A 635 ARG 0.004 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 590) hydrogen bonds : angle 4.79134 ( 1710) covalent geometry : bond 0.00443 (12345) covalent geometry : angle 0.65409 (16833) *********************** 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: 33 poor density : 77 time to evaluate : 1.375 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: 0.8858 (tpp) cc_final: 0.8593 (tpp) REVERT: A 471 HIS cc_start: 0.8832 (m170) cc_final: 0.8579 (m170) REVERT: A 775 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7898 (p) REVERT: B 166 MET cc_start: 0.8954 (mmm) cc_final: 0.8219 (mmm) REVERT: B 184 PHE cc_start: 0.6764 (t80) cc_final: 0.6124 (t80) REVERT: B 347 ASP cc_start: 0.7660 (p0) cc_final: 0.7301 (p0) REVERT: B 430 ASN cc_start: 0.8680 (t0) cc_final: 0.8457 (t0) REVERT: B 792 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8972 (tptt) outliers start: 33 outliers final: 14 residues processed: 102 average time/residue: 0.2616 time to fit residues: 39.1643 Evaluate side-chains 87 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 163 ARG Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 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 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 23 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.079201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.058174 restraints weight = 48638.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.058970 restraints weight = 26994.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.059009 restraints weight = 20339.146| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4228 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= 0.184 Angle : 0.642 11.668 16833 Z= 0.322 Chirality : 0.042 0.178 1912 Planarity : 0.005 0.048 2104 Dihedral : 15.870 143.289 1940 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.98 % Allowed : 17.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1456 helix: 1.12 (0.19), residues: 714 sheet: -0.63 (0.37), residues: 196 loop : -1.23 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 137 HIS 0.006 0.001 HIS B 760 PHE 0.019 0.002 PHE A 467 TYR 0.018 0.002 TYR B 635 ARG 0.008 0.000 ARG A 491 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 590) hydrogen bonds : angle 4.74831 ( 1710) covalent geometry : bond 0.00415 (12345) covalent geometry : angle 0.64184 (16833) *********************** 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 96 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 1.316 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: 0.8723 (tpp) cc_final: 0.8452 (tpp) REVERT: B 166 MET cc_start: 0.9059 (mmm) cc_final: 0.8384 (mmm) REVERT: B 184 PHE cc_start: 0.6999 (t80) cc_final: 0.6165 (t80) REVERT: B 347 ASP cc_start: 0.7698 (p0) cc_final: 0.7323 (p0) REVERT: B 430 ASN cc_start: 0.8705 (t0) cc_final: 0.8434 (t0) REVERT: B 792 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.9023 (tptt) outliers start: 24 outliers final: 13 residues processed: 90 average time/residue: 0.2902 time to fit residues: 37.4244 Evaluate side-chains 83 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 467 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 556 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.079006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.057686 restraints weight = 48221.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058639 restraints weight = 27710.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.058804 restraints weight = 21237.521| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12345 Z= 0.174 Angle : 0.643 12.604 16833 Z= 0.319 Chirality : 0.042 0.190 1912 Planarity : 0.004 0.048 2104 Dihedral : 15.863 140.685 1940 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.15 % Allowed : 17.44 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1456 helix: 1.16 (0.19), residues: 714 sheet: -0.69 (0.39), residues: 183 loop : -1.29 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 709 HIS 0.008 0.001 HIS B 760 PHE 0.013 0.002 PHE B 143 TYR 0.018 0.002 TYR B 635 ARG 0.009 0.000 ARG A 361 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 590) hydrogen bonds : angle 4.72560 ( 1710) covalent geometry : bond 0.00395 (12345) covalent geometry : angle 0.64312 (16833) *********************** 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 97 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 1.361 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 33 MET cc_start: 0.8614 (tpp) cc_final: 0.8319 (tpp) REVERT: A 184 PHE cc_start: 0.2837 (m-10) cc_final: 0.1194 (m-10) REVERT: A 187 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7983 (mmm) REVERT: B 347 ASP cc_start: 0.7641 (p0) cc_final: 0.7270 (p0) REVERT: B 430 ASN cc_start: 0.8598 (t0) cc_final: 0.8366 (t0) REVERT: B 624 MET cc_start: 0.8432 (mmm) cc_final: 0.8084 (mmm) REVERT: B 792 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.9037 (tptt) outliers start: 26 outliers final: 16 residues processed: 88 average time/residue: 0.2804 time to fit residues: 35.7358 Evaluate side-chains 88 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 187 MET 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 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 467 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 785 VAL 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 22 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 88 optimal weight: 0.0470 chunk 121 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 40 optimal weight: 0.0670 chunk 116 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.079133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.057684 restraints weight = 48379.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.058894 restraints weight = 27748.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.059370 restraints weight = 18946.265| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12345 Z= 0.158 Angle : 0.645 13.938 16833 Z= 0.318 Chirality : 0.041 0.171 1912 Planarity : 0.004 0.048 2104 Dihedral : 15.759 139.406 1940 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.74 % Allowed : 18.18 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1456 helix: 1.26 (0.19), residues: 710 sheet: -0.65 (0.39), residues: 178 loop : -1.29 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 709 HIS 0.014 0.001 HIS A 471 PHE 0.030 0.002 PHE A 467 TYR 0.018 0.001 TYR B 635 ARG 0.005 0.000 ARG A 361 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 590) hydrogen bonds : angle 4.67091 ( 1710) covalent geometry : bond 0.00358 (12345) covalent geometry : angle 0.64465 (16833) *********************** 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 : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.7338 (mtm) cc_final: 0.6950 (mpp) REVERT: A 184 PHE cc_start: 0.3082 (m-10) cc_final: 0.1715 (m-10) REVERT: A 187 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8117 (mmt) REVERT: B 166 MET cc_start: 0.9260 (mmm) cc_final: 0.8526 (mmm) REVERT: B 347 ASP cc_start: 0.7606 (p0) cc_final: 0.7241 (p0) REVERT: B 430 ASN cc_start: 0.8646 (t0) cc_final: 0.8238 (t0) REVERT: B 624 MET cc_start: 0.8382 (mmm) cc_final: 0.7948 (mmm) REVERT: B 792 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9026 (tptt) outliers start: 21 outliers final: 14 residues processed: 87 average time/residue: 0.2848 time to fit residues: 36.2350 Evaluate side-chains 87 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 1.471 ------------------------------------------------------------------------------- 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 187 MET Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 162 ASP 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 467 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 727 THR 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 110 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.078342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.056479 restraints weight = 48615.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.057618 restraints weight = 27751.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.057977 restraints weight = 18545.779| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12345 Z= 0.145 Angle : 0.627 12.743 16833 Z= 0.310 Chirality : 0.041 0.174 1912 Planarity : 0.004 0.048 2104 Dihedral : 15.665 137.074 1940 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.90 % Allowed : 18.02 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1456 helix: 1.34 (0.19), residues: 711 sheet: -0.59 (0.39), residues: 183 loop : -1.26 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 709 HIS 0.005 0.001 HIS B 760 PHE 0.009 0.001 PHE A 184 TYR 0.018 0.001 TYR B 635 ARG 0.004 0.000 ARG A 361 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 590) hydrogen bonds : angle 4.58047 ( 1710) covalent geometry : bond 0.00327 (12345) covalent geometry : angle 0.62742 (16833) *********************** 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 98 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 1.456 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 68 MET cc_start: 0.8367 (ptm) cc_final: 0.7775 (ppp) REVERT: A 184 PHE cc_start: 0.3002 (m-10) cc_final: 0.1732 (m-10) REVERT: A 187 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8003 (mmt) REVERT: B 166 MET cc_start: 0.9275 (mmm) cc_final: 0.8587 (mmm) REVERT: B 184 PHE cc_start: 0.7056 (t80) cc_final: 0.6230 (t80) REVERT: B 347 ASP cc_start: 0.7688 (p0) cc_final: 0.7354 (p0) REVERT: B 624 MET cc_start: 0.8366 (mmm) cc_final: 0.7922 (mmm) REVERT: B 792 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.9038 (tptt) outliers start: 23 outliers final: 16 residues processed: 89 average time/residue: 0.2769 time to fit residues: 35.4017 Evaluate side-chains 88 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 471 HIS 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 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 467 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 792 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 125 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS B 339 GLN B 557 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.079138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.057328 restraints weight = 48482.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.058529 restraints weight = 27683.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.058848 restraints weight = 18302.726| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4784 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= 0.123 Angle : 0.620 13.635 16833 Z= 0.304 Chirality : 0.040 0.174 1912 Planarity : 0.004 0.049 2104 Dihedral : 15.597 139.482 1940 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.49 % Allowed : 18.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1456 helix: 1.45 (0.19), residues: 715 sheet: -0.52 (0.39), residues: 185 loop : -1.21 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 202 HIS 0.008 0.001 HIS A 471 PHE 0.011 0.001 PHE A 184 TYR 0.032 0.002 TYR A 473 ARG 0.003 0.000 ARG A 361 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 590) hydrogen bonds : angle 4.50394 ( 1710) covalent geometry : bond 0.00273 (12345) covalent geometry : angle 0.61987 (16833) ********************** 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 92 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.7286 (mtm) cc_final: 0.6891 (mpp) REVERT: A 68 MET cc_start: 0.8342 (ptm) cc_final: 0.7778 (ppp) REVERT: A 184 PHE cc_start: 0.3007 (m-10) cc_final: 0.1889 (m-10) REVERT: A 187 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8207 (mmt) REVERT: A 790 ARG cc_start: 0.7517 (mmt180) cc_final: 0.7314 (mmt90) REVERT: B 166 MET cc_start: 0.9247 (mmm) cc_final: 0.8544 (mmm) REVERT: B 184 PHE cc_start: 0.6824 (t80) cc_final: 0.6325 (t80) REVERT: B 347 ASP cc_start: 0.7611 (p0) cc_final: 0.7261 (p0) REVERT: B 624 MET cc_start: 0.8366 (mmm) cc_final: 0.7916 (mmm) REVERT: B 792 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9012 (tptt) outliers start: 18 outliers final: 11 residues processed: 86 average time/residue: 0.4285 time to fit residues: 54.0583 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 : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 187 MET 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 375 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 792 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 113 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 4 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.078922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.057730 restraints weight = 48085.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.058718 restraints weight = 27568.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.059319 restraints weight = 19108.154| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12345 Z= 0.133 Angle : 0.625 13.606 16833 Z= 0.307 Chirality : 0.040 0.174 1912 Planarity : 0.004 0.051 2104 Dihedral : 15.565 142.272 1940 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.32 % Allowed : 18.43 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1456 helix: 1.52 (0.19), residues: 709 sheet: -0.54 (0.39), residues: 187 loop : -1.18 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 137 HIS 0.005 0.001 HIS B 760 PHE 0.018 0.001 PHE A 204 TYR 0.025 0.001 TYR A 243 ARG 0.003 0.000 ARG A 361 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 590) hydrogen bonds : angle 4.45811 ( 1710) covalent geometry : bond 0.00302 (12345) covalent geometry : angle 0.62532 (16833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4084.88 seconds wall clock time: 74 minutes 46.01 seconds (4486.01 seconds total)