Starting phenix.real_space_refine on Thu Feb 5 05:14:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzh_24760/02_2026/7rzh_24760.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzh_24760/02_2026/7rzh_24760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rzh_24760/02_2026/7rzh_24760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzh_24760/02_2026/7rzh_24760.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rzh_24760/02_2026/7rzh_24760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzh_24760/02_2026/7rzh_24760.map" } resolution = 3.8 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= -0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 9866 2.51 5 N 2559 2.21 5 O 2832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15300 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7637 Classifications: {'peptide': 932} Link IDs: {'PTRANS': 49, 'TRANS': 882} Chain breaks: 1 Chain: "B" Number of atoms: 7663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 935, 7663 Classifications: {'peptide': 935} Link IDs: {'PTRANS': 48, 'TRANS': 886} Chain breaks: 1 Time building chain proxies: 3.23, per 1000 atoms: 0.21 Number of scatterers: 15300 At special positions: 0 Unit cell: (114.925, 137.693, 169.135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 2832 8.00 N 2559 7.00 C 9866 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 477.7 milliseconds 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 10 sheets defined 51.4% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 105 through 116 removed outlier: 3.573A pdb=" N HIS A 112 " --> pdb=" O HIS A 108 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU A 116 " --> pdb=" O HIS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.646A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 196 removed outlier: 3.873A pdb=" N ASN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 209 removed outlier: 3.764A pdb=" N GLY A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 236 through 248 Processing helix chain 'A' and resid 263 through 275 removed outlier: 3.786A pdb=" N LEU A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.700A pdb=" N TYR A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 removed outlier: 3.595A pdb=" N TYR A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 386 Processing helix chain 'A' and resid 386 through 405 Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.622A pdb=" N PHE A 411 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 442 removed outlier: 3.860A pdb=" N HIS A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'A' and resid 460 through 471 removed outlier: 3.554A pdb=" N ILE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 486 removed outlier: 4.117A pdb=" N GLU A 486 " --> pdb=" O LYS A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 506 through 516 Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.682A pdb=" N ALA A 583 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 584 " --> pdb=" O PRO A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 615 removed outlier: 4.685A pdb=" N GLU A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N TYR A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 611 " --> pdb=" O TYR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 Processing helix chain 'A' and resid 655 through 673 Processing helix chain 'A' and resid 677 through 691 removed outlier: 3.581A pdb=" N LEU A 689 " --> pdb=" O TYR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 707 Processing helix chain 'A' and resid 708 through 722 Proline residue: A 717 - end of helix removed outlier: 4.388A pdb=" N ARG A 722 " --> pdb=" O GLN A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 754 Processing helix chain 'A' and resid 801 through 823 removed outlier: 4.069A pdb=" N GLU A 817 " --> pdb=" O GLN A 813 " (cutoff:3.500A) Proline residue: A 818 - end of helix removed outlier: 3.631A pdb=" N ASN A 821 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 877 Processing helix chain 'A' and resid 878 through 894 Processing helix chain 'A' and resid 899 through 914 removed outlier: 3.707A pdb=" N GLU A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 910 " --> pdb=" O LYS A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 931 removed outlier: 4.210A pdb=" N THR A 923 " --> pdb=" O ASP A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 943 Processing helix chain 'A' and resid 994 through 1002 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 134 removed outlier: 3.856A pdb=" N SER B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 171 removed outlier: 3.644A pdb=" N PHE B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 169 " --> pdb=" O PHE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 195 removed outlier: 3.819A pdb=" N ARG B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 227 through 234 removed outlier: 3.645A pdb=" N GLN B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 248 Processing helix chain 'B' and resid 263 through 277 removed outlier: 3.750A pdb=" N LEU B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU B 277 " --> pdb=" O LYS B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 380 through 386 Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 407 through 424 removed outlier: 3.731A pdb=" N PHE B 411 " --> pdb=" O GLN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 444 removed outlier: 3.722A pdb=" N HIS B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR B 443 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 453 removed outlier: 4.675A pdb=" N GLU B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 471 Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 581 through 585 removed outlier: 3.567A pdb=" N TYR B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 608 removed outlier: 4.345A pdb=" N GLU B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 Processing helix chain 'B' and resid 637 through 651 removed outlier: 3.811A pdb=" N LEU B 641 " --> pdb=" O LYS B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 675 removed outlier: 3.818A pdb=" N ARG B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 691 Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 708 through 722 Proline residue: B 717 - end of helix removed outlier: 4.042A pdb=" N ARG B 722 " --> pdb=" O GLN B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 754 Processing helix chain 'B' and resid 801 through 822 removed outlier: 4.041A pdb=" N GLU B 817 " --> pdb=" O GLN B 813 " (cutoff:3.500A) Proline residue: B 818 - end of helix Processing helix chain 'B' and resid 855 through 877 Processing helix chain 'B' and resid 878 through 894 Processing helix chain 'B' and resid 899 through 913 removed outlier: 3.869A pdb=" N TYR B 907 " --> pdb=" O GLU B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 931 removed outlier: 3.678A pdb=" N ALA B 926 " --> pdb=" O ASN B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 943 Processing helix chain 'B' and resid 994 through 1002 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 3.864A pdb=" N ARG A 65 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.665A pdb=" N VAL A 377 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 372 " --> pdb=" O LYS A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.665A pdb=" N VAL A 377 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN A 499 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 549 through 553 removed outlier: 6.783A pdb=" N LEU A 550 " --> pdb=" O PHE A 561 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE A 561 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS A 552 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP A 560 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N GLY A 731 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 775 through 782 removed outlier: 6.209A pdb=" N GLY A 775 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N SER A 955 " --> pdb=" O GLY A 775 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE A 777 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N HIS A 957 " --> pdb=" O PHE A 777 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR A 779 " --> pdb=" O HIS A 957 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A 959 " --> pdb=" O TYR A 779 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN A 781 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS A 952 " --> pdb=" O GLN A 796 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLN A 844 " --> pdb=" O THR A 797 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A 847 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 836 " --> pdb=" O ARG A 847 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 849 " --> pdb=" O PHE A 834 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 851 " --> pdb=" O ILE A 832 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 832 " --> pdb=" O GLN A 851 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 63 through 68 removed outlier: 6.382A pdb=" N LYS B 74 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N VAL B 258 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU B 76 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 88 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE B 151 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 90 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR B 149 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 365 removed outlier: 3.794A pdb=" N ILE B 375 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN B 312 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR B 302 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN B 499 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 549 through 553 removed outlier: 7.439A pdb=" N LEU B 559 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASP B 553 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS B 558 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU B 729 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP B 560 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 628 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 621 " --> pdb=" O TYR B 628 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 776 through 782 removed outlier: 6.089A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR B 779 " --> pdb=" O HIS B 957 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU B 959 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLN B 781 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 850 " --> pdb=" O ILE B 791 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE B 832 " --> pdb=" O GLN B 851 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 776 through 782 removed outlier: 6.089A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR B 779 " --> pdb=" O HIS B 957 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU B 959 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLN B 781 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 850 " --> pdb=" O ILE B 791 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 847 " --> pdb=" O GLY B 836 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY B 836 " --> pdb=" O ARG B 847 " (cutoff:3.500A) 781 hydrogen bonds defined for protein. 2247 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2955 1.33 - 1.45: 3776 1.45 - 1.57: 8864 1.57 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 15681 Sorted by residual: bond pdb=" N VAL B 305 " pdb=" CA VAL B 305 " ideal model delta sigma weight residual 1.458 1.492 -0.035 7.70e-03 1.69e+04 2.01e+01 bond pdb=" N ASP B 586 " pdb=" CA ASP B 586 " ideal model delta sigma weight residual 1.453 1.490 -0.037 8.30e-03 1.45e+04 1.98e+01 bond pdb=" N VAL B 283 " pdb=" CA VAL B 283 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.60e-03 1.73e+04 1.96e+01 bond pdb=" N VAL B 785 " pdb=" CA VAL B 785 " ideal model delta sigma weight residual 1.456 1.498 -0.041 9.50e-03 1.11e+04 1.90e+01 bond pdb=" N LYS A 854 " pdb=" CA LYS A 854 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.84e+01 ... (remaining 15676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 15084 1.63 - 3.26: 5521 3.26 - 4.89: 537 4.89 - 6.52: 58 6.52 - 8.15: 5 Bond angle restraints: 21205 Sorted by residual: angle pdb=" N PHE B 115 " pdb=" CA PHE B 115 " pdb=" C PHE B 115 " ideal model delta sigma weight residual 113.72 106.21 7.51 1.30e+00 5.92e-01 3.34e+01 angle pdb=" CA ASP A 91 " pdb=" C ASP A 91 " pdb=" O ASP A 91 " ideal model delta sigma weight residual 121.33 115.36 5.97 1.08e+00 8.57e-01 3.06e+01 angle pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" O GLY A 221 " ideal model delta sigma weight residual 122.29 117.96 4.33 8.10e-01 1.52e+00 2.85e+01 angle pdb=" N LYS A 281 " pdb=" CA LYS A 281 " pdb=" C LYS A 281 " ideal model delta sigma weight residual 113.16 106.80 6.36 1.24e+00 6.50e-01 2.63e+01 angle pdb=" N PRO A 587 " pdb=" CA PRO A 587 " pdb=" C PRO A 587 " ideal model delta sigma weight residual 113.53 106.49 7.04 1.39e+00 5.18e-01 2.57e+01 ... (remaining 21200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 8568 17.86 - 35.72: 675 35.72 - 53.58: 206 53.58 - 71.43: 32 71.43 - 89.29: 8 Dihedral angle restraints: 9489 sinusoidal: 3980 harmonic: 5509 Sorted by residual: dihedral pdb=" C THR B 118 " pdb=" N THR B 118 " pdb=" CA THR B 118 " pdb=" CB THR B 118 " ideal model delta harmonic sigma weight residual -122.00 -138.28 16.28 0 2.50e+00 1.60e-01 4.24e+01 dihedral pdb=" C TYR A 326 " pdb=" N TYR A 326 " pdb=" CA TYR A 326 " pdb=" CB TYR A 326 " ideal model delta harmonic sigma weight residual -122.60 -134.96 12.36 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" C ASN B 282 " pdb=" N ASN B 282 " pdb=" CA ASN B 282 " pdb=" CB ASN B 282 " ideal model delta harmonic sigma weight residual -122.60 -134.39 11.79 0 2.50e+00 1.60e-01 2.22e+01 ... (remaining 9486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1331 0.093 - 0.187: 794 0.187 - 0.280: 145 0.280 - 0.373: 7 0.373 - 0.467: 2 Chirality restraints: 2279 Sorted by residual: chirality pdb=" CA THR B 118 " pdb=" N THR B 118 " pdb=" C THR B 118 " pdb=" CB THR B 118 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CA TYR A 326 " pdb=" N TYR A 326 " pdb=" C TYR A 326 " pdb=" CB TYR A 326 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA ARG A 229 " pdb=" N ARG A 229 " pdb=" C ARG A 229 " pdb=" CB ARG A 229 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 2276 not shown) Planarity restraints: 2742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 114 " -0.021 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C LEU B 114 " 0.074 2.00e-02 2.50e+03 pdb=" O LEU B 114 " -0.028 2.00e-02 2.50e+03 pdb=" N PHE B 115 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 91 " 0.014 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C ASP A 91 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP A 91 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL A 92 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 941 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C LYS B 941 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS B 941 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU B 942 " -0.014 2.00e-02 2.50e+03 ... (remaining 2739 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 20 2.46 - 3.07: 9878 3.07 - 3.68: 23640 3.68 - 4.29: 34439 4.29 - 4.90: 56057 Nonbonded interactions: 124034 Sorted by model distance: nonbonded pdb=" CE1 PHE A 115 " pdb=" CD2 TYR A 127 " model vdw 1.853 3.640 nonbonded pdb=" CZ PHE B 317 " pdb=" CG2 VAL B 476 " model vdw 1.993 3.760 nonbonded pdb=" OE1 GLU B 529 " pdb=" NZ LYS B 644 " model vdw 2.081 3.120 nonbonded pdb=" CD2 LEU B 771 " pdb=" CA HIS B 952 " model vdw 2.090 3.890 nonbonded pdb=" CE1 PHE B 317 " pdb=" CG2 VAL B 476 " model vdw 2.150 3.760 ... (remaining 124029 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 57 through 959 or resid 991 through 1009)) selection = (chain 'B' and resid 57 through 1009) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.030 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.960 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5423 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 : 0.012 0.045 15682 Z= 0.964 Angle : 1.501 8.149 21205 Z= 1.176 Chirality : 0.107 0.467 2279 Planarity : 0.004 0.043 2742 Dihedral : 14.190 89.294 5929 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.58 % Favored : 97.26 % Rotamer: Outliers : 5.29 % Allowed : 8.71 % Favored : 86.01 % Cbeta Deviations : 0.34 % 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: 2.98 (0.19), residues: 1859 helix: 3.45 (0.17), residues: 861 sheet: 2.11 (0.28), residues: 322 loop : -0.14 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 402 TYR 0.014 0.002 TYR B 779 PHE 0.020 0.002 PHE B 130 TRP 0.012 0.002 TRP B 560 HIS 0.011 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.01238 (15681) covalent geometry : angle 1.50057 (21205) hydrogen bonds : bond 0.21207 ( 765) hydrogen bonds : angle 7.44163 ( 2247) Misc. bond : bond 0.01397 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 435 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 THR cc_start: 0.5699 (m) cc_final: 0.4876 (m) REVERT: A 371 MET cc_start: 0.2235 (mmm) cc_final: 0.1906 (mmm) REVERT: A 385 LEU cc_start: 0.7020 (mm) cc_final: 0.6787 (mm) REVERT: A 672 ASN cc_start: 0.7436 (t0) cc_final: 0.7164 (t0) REVERT: A 963 MET cc_start: 0.3184 (ttm) cc_final: 0.2824 (tmm) REVERT: B 61 LYS cc_start: 0.3613 (OUTLIER) cc_final: 0.3050 (tmtt) REVERT: B 199 TRP cc_start: 0.5883 (t-100) cc_final: 0.5491 (t-100) REVERT: B 215 PHE cc_start: 0.6409 (t80) cc_final: 0.5959 (t80) REVERT: B 279 GLU cc_start: 0.5509 (tp30) cc_final: 0.5279 (tp30) REVERT: B 307 ILE cc_start: 0.4184 (mt) cc_final: 0.3551 (tt) REVERT: B 687 ARG cc_start: 0.7101 (ptp-170) cc_final: 0.6637 (tmt-80) REVERT: B 706 ASP cc_start: 0.6694 (p0) cc_final: 0.6241 (p0) outliers start: 88 outliers final: 13 residues processed: 501 average time/residue: 0.1177 time to fit residues: 86.9892 Evaluate side-chains 248 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 234 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 759 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0030 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 overall best weight: 2.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 300 GLN A 340 HIS A 534 ASN A 573 ASN A 638 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 ASN ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 146 HIS B 184 ASN B 312 ASN B 418 ASN B 514 GLN B 515 ASN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 GLN B 821 ASN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 GLN B 922 ASN B 993 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.156492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.134224 restraints weight = 47517.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.134202 restraints weight = 28681.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.135671 restraints weight = 21933.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.135997 restraints weight = 16353.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.136167 restraints weight = 15568.223| |-----------------------------------------------------------------------------| r_work (final): 0.4757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15682 Z= 0.191 Angle : 0.746 15.553 21205 Z= 0.390 Chirality : 0.047 0.249 2279 Planarity : 0.005 0.100 2742 Dihedral : 5.460 46.140 2057 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.14 % Allowed : 16.40 % Favored : 79.46 % 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: 1.51 (0.19), residues: 1859 helix: 1.67 (0.16), residues: 895 sheet: 1.49 (0.27), residues: 352 loop : -0.23 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 711 TYR 0.029 0.002 TYR A 500 PHE 0.048 0.003 PHE A 715 TRP 0.018 0.002 TRP B 513 HIS 0.007 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00407 (15681) covalent geometry : angle 0.74577 (21205) hydrogen bonds : bond 0.06629 ( 765) hydrogen bonds : angle 6.10019 ( 2247) Misc. bond : bond 0.00624 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 242 time to evaluate : 0.640 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 385 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6708 (mm) REVERT: A 963 MET cc_start: 0.3473 (ttm) cc_final: 0.2850 (tmm) REVERT: B 54 ILE cc_start: 0.4696 (OUTLIER) cc_final: 0.4404 (mt) REVERT: B 102 ASN cc_start: 0.6367 (p0) cc_final: 0.5541 (p0) REVERT: B 119 LYS cc_start: 0.8170 (tptt) cc_final: 0.7907 (tppt) REVERT: B 199 TRP cc_start: 0.6235 (t-100) cc_final: 0.5589 (t-100) REVERT: B 227 GLU cc_start: -0.1893 (OUTLIER) cc_final: -0.2552 (tp30) REVERT: B 240 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7286 (mt-10) REVERT: B 279 GLU cc_start: 0.6085 (tp30) cc_final: 0.5592 (tp30) REVERT: B 297 HIS cc_start: 0.4945 (OUTLIER) cc_final: 0.4507 (m-70) REVERT: B 307 ILE cc_start: 0.4639 (mt) cc_final: 0.3962 (tt) REVERT: B 337 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7159 (tp) REVERT: B 706 ASP cc_start: 0.7297 (p0) cc_final: 0.6663 (p0) REVERT: B 1011 HIS cc_start: 0.4055 (OUTLIER) cc_final: 0.3636 (t-170) outliers start: 69 outliers final: 30 residues processed: 290 average time/residue: 0.1143 time to fit residues: 51.2893 Evaluate side-chains 234 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 955 SER Chi-restraints excluded: chain B residue 1011 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 59 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 111 optimal weight: 0.0020 chunk 98 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 169 optimal weight: 8.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 672 ASN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 HIS B 917 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.153415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.130754 restraints weight = 48438.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.130407 restraints weight = 27726.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.132335 restraints weight = 21391.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.132231 restraints weight = 16467.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.132453 restraints weight = 15215.736| |-----------------------------------------------------------------------------| r_work (final): 0.4683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15682 Z= 0.180 Angle : 0.693 12.078 21205 Z= 0.363 Chirality : 0.045 0.212 2279 Planarity : 0.006 0.165 2742 Dihedral : 5.444 51.023 2047 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.74 % Allowed : 18.14 % Favored : 77.12 % 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: 0.87 (0.19), residues: 1859 helix: 1.14 (0.16), residues: 895 sheet: 0.97 (0.28), residues: 349 loop : -0.39 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 62 TYR 0.031 0.002 TYR A 666 PHE 0.044 0.002 PHE A 715 TRP 0.008 0.002 TRP B 908 HIS 0.007 0.001 HIS B 681 Details of bonding type rmsd covalent geometry : bond 0.00385 (15681) covalent geometry : angle 0.69334 (21205) hydrogen bonds : bond 0.05471 ( 765) hydrogen bonds : angle 5.61394 ( 2247) Misc. bond : bond 0.00572 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 208 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.2084 (mmm) cc_final: 0.1693 (mmm) REVERT: A 385 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6779 (mm) REVERT: A 440 ILE cc_start: 0.5492 (OUTLIER) cc_final: 0.5206 (pt) REVERT: A 672 ASN cc_start: 0.8111 (t0) cc_final: 0.7744 (t0) REVERT: A 877 MET cc_start: 0.1790 (ttm) cc_final: 0.1146 (mtt) REVERT: B 102 ASN cc_start: 0.6622 (p0) cc_final: 0.5727 (p0) REVERT: B 199 TRP cc_start: 0.6368 (t-100) cc_final: 0.5704 (t-100) REVERT: B 227 GLU cc_start: -0.1865 (OUTLIER) cc_final: -0.2541 (tp30) REVERT: B 240 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7242 (mt-10) REVERT: B 279 GLU cc_start: 0.6308 (tp30) cc_final: 0.5852 (tp30) REVERT: B 307 ILE cc_start: 0.4548 (mt) cc_final: 0.3815 (tt) REVERT: B 690 MET cc_start: 0.5386 (mmp) cc_final: 0.5129 (tpp) REVERT: B 706 ASP cc_start: 0.7561 (p0) cc_final: 0.7144 (p0) REVERT: B 1011 HIS cc_start: 0.4498 (OUTLIER) cc_final: 0.3981 (t-170) outliers start: 79 outliers final: 47 residues processed: 267 average time/residue: 0.1003 time to fit residues: 42.8278 Evaluate side-chains 231 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 955 SER Chi-restraints excluded: chain B residue 1011 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 9 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 166 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 GLN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 GLN A 952 HIS B 184 ASN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 396 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.147434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.125483 restraints weight = 48250.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.124963 restraints weight = 28472.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.126266 restraints weight = 22331.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.126524 restraints weight = 16692.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.126733 restraints weight = 16146.851| |-----------------------------------------------------------------------------| r_work (final): 0.4594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15682 Z= 0.228 Angle : 0.782 15.127 21205 Z= 0.407 Chirality : 0.048 0.224 2279 Planarity : 0.007 0.201 2742 Dihedral : 5.673 55.046 2041 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.77 % Allowed : 18.02 % Favored : 76.22 % 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 (0.18), residues: 1859 helix: 0.55 (0.16), residues: 883 sheet: 0.41 (0.27), residues: 334 loop : -0.71 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG B 62 TYR 0.031 0.003 TYR A 779 PHE 0.061 0.003 PHE A 715 TRP 0.014 0.002 TRP B 355 HIS 0.008 0.002 HIS A 885 Details of bonding type rmsd covalent geometry : bond 0.00511 (15681) covalent geometry : angle 0.78155 (21205) hydrogen bonds : bond 0.05819 ( 765) hydrogen bonds : angle 5.79095 ( 2247) Misc. bond : bond 0.00812 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 197 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 LEU cc_start: 0.7423 (mp) cc_final: 0.7201 (mp) REVERT: A 385 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6719 (mm) REVERT: A 462 ASP cc_start: 0.8652 (m-30) cc_final: 0.8367 (t0) REVERT: A 637 LYS cc_start: 0.3061 (OUTLIER) cc_final: 0.2528 (ptmt) REVERT: A 672 ASN cc_start: 0.8199 (t0) cc_final: 0.7689 (t0) REVERT: A 774 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6628 (tpt90) REVERT: B 102 ASN cc_start: 0.6595 (p0) cc_final: 0.6148 (p0) REVERT: B 119 LYS cc_start: 0.7701 (tppt) cc_final: 0.7103 (mmmt) REVERT: B 199 TRP cc_start: 0.6203 (t-100) cc_final: 0.5521 (t-100) REVERT: B 227 GLU cc_start: -0.2084 (OUTLIER) cc_final: -0.2793 (tp30) REVERT: B 240 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7185 (mt-10) REVERT: B 279 GLU cc_start: 0.6592 (tp30) cc_final: 0.6132 (tp30) REVERT: B 307 ILE cc_start: 0.4510 (mt) cc_final: 0.3859 (tp) REVERT: B 386 HIS cc_start: 0.6835 (OUTLIER) cc_final: 0.6412 (m90) REVERT: B 687 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6497 (tmt170) REVERT: B 706 ASP cc_start: 0.7732 (p0) cc_final: 0.7045 (p0) REVERT: B 907 TYR cc_start: 0.5154 (OUTLIER) cc_final: 0.4685 (m-10) REVERT: B 915 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7366 (mt0) outliers start: 96 outliers final: 58 residues processed: 273 average time/residue: 0.1044 time to fit residues: 44.0096 Evaluate side-chains 237 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 171 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 637 LYS Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 715 PHE Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 907 TYR Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 955 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 61 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 179 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 15 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 116 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.146439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.124031 restraints weight = 48493.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.123601 restraints weight = 28680.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.124723 restraints weight = 24107.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.125276 restraints weight = 17350.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.125588 restraints weight = 16164.358| |-----------------------------------------------------------------------------| r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15682 Z= 0.227 Angle : 0.771 14.094 21205 Z= 0.401 Chirality : 0.047 0.223 2279 Planarity : 0.007 0.238 2742 Dihedral : 5.714 53.496 2037 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.83 % Allowed : 19.40 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.18), residues: 1859 helix: 0.27 (0.16), residues: 880 sheet: 0.08 (0.27), residues: 335 loop : -0.86 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 62 TYR 0.025 0.003 TYR A 779 PHE 0.044 0.002 PHE A 715 TRP 0.014 0.002 TRP B 908 HIS 0.009 0.002 HIS A 885 Details of bonding type rmsd covalent geometry : bond 0.00507 (15681) covalent geometry : angle 0.77076 (21205) hydrogen bonds : bond 0.05658 ( 765) hydrogen bonds : angle 5.85858 ( 2247) Misc. bond : bond 0.01387 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 181 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 LEU cc_start: 0.7484 (mp) cc_final: 0.7218 (mp) REVERT: A 385 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6826 (mm) REVERT: A 462 ASP cc_start: 0.8978 (m-30) cc_final: 0.8612 (t0) REVERT: A 477 ARG cc_start: 0.6817 (tmm160) cc_final: 0.6513 (tmm160) REVERT: A 566 LYS cc_start: 0.5496 (OUTLIER) cc_final: 0.5100 (ptpt) REVERT: A 672 ASN cc_start: 0.8272 (t0) cc_final: 0.8037 (t0) REVERT: A 915 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: A 997 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: A 1005 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6927 (m-80) REVERT: B 113 MET cc_start: 0.1501 (ttt) cc_final: 0.1146 (ttt) REVERT: B 119 LYS cc_start: 0.7800 (tppt) cc_final: 0.7082 (mmmt) REVERT: B 184 ASN cc_start: 0.5274 (m-40) cc_final: 0.4823 (p0) REVERT: B 199 TRP cc_start: 0.6409 (t-100) cc_final: 0.5738 (t-100) REVERT: B 227 GLU cc_start: -0.1875 (OUTLIER) cc_final: -0.2651 (tp30) REVERT: B 240 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7019 (mt-10) REVERT: B 279 GLU cc_start: 0.6832 (tp30) cc_final: 0.6349 (tp30) REVERT: B 386 HIS cc_start: 0.7000 (OUTLIER) cc_final: 0.6615 (m90) REVERT: B 521 LYS cc_start: 0.5618 (OUTLIER) cc_final: 0.5035 (pttm) REVERT: B 574 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8191 (mt) REVERT: B 589 HIS cc_start: 0.5933 (OUTLIER) cc_final: 0.5358 (m90) REVERT: B 687 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6533 (tmt170) REVERT: B 706 ASP cc_start: 0.7827 (p0) cc_final: 0.7149 (p0) REVERT: B 907 TYR cc_start: 0.5302 (OUTLIER) cc_final: 0.4778 (m-10) REVERT: B 915 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7290 (mt0) outliers start: 97 outliers final: 60 residues processed: 257 average time/residue: 0.1065 time to fit residues: 42.3012 Evaluate side-chains 238 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 165 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 589 HIS Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 637 LYS Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 715 PHE Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 907 TYR Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 955 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 151 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.2980 chunk 90 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.147444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.125808 restraints weight = 47990.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.125739 restraints weight = 29860.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.127175 restraints weight = 22666.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.127345 restraints weight = 16403.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.127565 restraints weight = 15802.476| |-----------------------------------------------------------------------------| r_work (final): 0.4613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15682 Z= 0.170 Angle : 0.696 10.973 21205 Z= 0.361 Chirality : 0.044 0.210 2279 Planarity : 0.007 0.272 2742 Dihedral : 5.554 50.075 2037 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.41 % Allowed : 20.18 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.18), residues: 1859 helix: 0.43 (0.16), residues: 879 sheet: -0.06 (0.27), residues: 345 loop : -0.81 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 668 TYR 0.024 0.002 TYR A 779 PHE 0.056 0.002 PHE A 715 TRP 0.011 0.002 TRP B 908 HIS 0.006 0.001 HIS A 885 Details of bonding type rmsd covalent geometry : bond 0.00378 (15681) covalent geometry : angle 0.69644 (21205) hydrogen bonds : bond 0.05159 ( 765) hydrogen bonds : angle 5.62056 ( 2247) Misc. bond : bond 0.00791 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 182 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 LEU cc_start: 0.7539 (mp) cc_final: 0.7300 (mp) REVERT: A 385 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6729 (mm) REVERT: A 444 TYR cc_start: 0.4929 (OUTLIER) cc_final: 0.4460 (m-10) REVERT: A 462 ASP cc_start: 0.8697 (m-30) cc_final: 0.8438 (t0) REVERT: A 637 LYS cc_start: 0.3019 (OUTLIER) cc_final: 0.2633 (ptmt) REVERT: A 997 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: B 113 MET cc_start: 0.1451 (ttt) cc_final: 0.0885 (ttt) REVERT: B 119 LYS cc_start: 0.7966 (tppt) cc_final: 0.6992 (mmmt) REVERT: B 227 GLU cc_start: -0.1931 (OUTLIER) cc_final: -0.2582 (tp30) REVERT: B 240 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7124 (mt-10) REVERT: B 279 GLU cc_start: 0.6643 (tp30) cc_final: 0.6197 (tp30) REVERT: B 291 HIS cc_start: 0.5751 (p-80) cc_final: 0.4716 (t70) REVERT: B 386 HIS cc_start: 0.6690 (OUTLIER) cc_final: 0.6284 (m90) REVERT: B 574 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8161 (mt) REVERT: B 589 HIS cc_start: 0.5844 (OUTLIER) cc_final: 0.5265 (m90) REVERT: B 687 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6493 (tmt170) REVERT: B 706 ASP cc_start: 0.7488 (p0) cc_final: 0.7066 (p0) REVERT: B 806 MET cc_start: 0.6237 (mmp) cc_final: 0.5824 (mmt) REVERT: B 915 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7068 (mt0) outliers start: 90 outliers final: 63 residues processed: 251 average time/residue: 0.1061 time to fit residues: 41.6481 Evaluate side-chains 234 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 161 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 589 HIS Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 637 LYS Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 715 PHE Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 955 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 82 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 96 optimal weight: 0.1980 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.146073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.123387 restraints weight = 48242.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.124216 restraints weight = 29188.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.125178 restraints weight = 21828.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.125247 restraints weight = 16468.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.125438 restraints weight = 15238.316| |-----------------------------------------------------------------------------| r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15682 Z= 0.193 Angle : 0.731 11.200 21205 Z= 0.376 Chirality : 0.046 0.270 2279 Planarity : 0.007 0.279 2742 Dihedral : 5.629 49.787 2036 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 6.37 % Allowed : 20.00 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.18), residues: 1859 helix: 0.36 (0.16), residues: 868 sheet: -0.20 (0.27), residues: 341 loop : -0.96 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 62 TYR 0.023 0.002 TYR A 779 PHE 0.045 0.002 PHE A 715 TRP 0.019 0.002 TRP B 513 HIS 0.007 0.001 HIS B 393 Details of bonding type rmsd covalent geometry : bond 0.00435 (15681) covalent geometry : angle 0.73061 (21205) hydrogen bonds : bond 0.05291 ( 765) hydrogen bonds : angle 5.63414 ( 2247) Misc. bond : bond 0.00526 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 171 time to evaluate : 0.679 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 337 LEU cc_start: 0.7723 (mp) cc_final: 0.7429 (mp) REVERT: A 385 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6717 (mm) REVERT: A 444 TYR cc_start: 0.5165 (OUTLIER) cc_final: 0.4668 (m-10) REVERT: A 462 ASP cc_start: 0.8920 (m-30) cc_final: 0.8646 (t0) REVERT: A 620 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7240 (mt) REVERT: A 637 LYS cc_start: 0.2928 (OUTLIER) cc_final: 0.2684 (ptmt) REVERT: A 877 MET cc_start: 0.2062 (ttm) cc_final: 0.1799 (mtt) REVERT: A 997 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: A 1005 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6783 (m-80) REVERT: B 113 MET cc_start: 0.1280 (ttt) cc_final: 0.0812 (ttt) REVERT: B 119 LYS cc_start: 0.7834 (tppt) cc_final: 0.7064 (mmmt) REVERT: B 227 GLU cc_start: -0.1944 (OUTLIER) cc_final: -0.2675 (tp30) REVERT: B 240 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7082 (mt-10) REVERT: B 279 GLU cc_start: 0.6814 (tp30) cc_final: 0.6325 (tp30) REVERT: B 291 HIS cc_start: 0.5819 (OUTLIER) cc_final: 0.4865 (t70) REVERT: B 307 ILE cc_start: 0.4529 (OUTLIER) cc_final: 0.3799 (tp) REVERT: B 386 HIS cc_start: 0.6888 (OUTLIER) cc_final: 0.6478 (m90) REVERT: B 425 LYS cc_start: 0.7935 (mmtp) cc_final: 0.7643 (mmmt) REVERT: B 454 TYR cc_start: 0.7163 (m-10) cc_final: 0.6833 (m-10) REVERT: B 521 LYS cc_start: 0.6083 (OUTLIER) cc_final: 0.5388 (pttm) REVERT: B 574 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8179 (mt) REVERT: B 589 HIS cc_start: 0.6108 (OUTLIER) cc_final: 0.5436 (m90) REVERT: B 687 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6461 (tmt170) REVERT: B 706 ASP cc_start: 0.7638 (p0) cc_final: 0.6946 (p0) REVERT: B 858 TYR cc_start: 0.6469 (t80) cc_final: 0.6093 (t80) REVERT: B 907 TYR cc_start: 0.5373 (OUTLIER) cc_final: 0.4886 (m-10) REVERT: B 915 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7160 (mt0) outliers start: 106 outliers final: 73 residues processed: 256 average time/residue: 0.1061 time to fit residues: 42.5505 Evaluate side-chains 246 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 157 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 844 GLN Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 589 HIS Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 637 LYS Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 715 PHE Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 798 ASP Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 907 TYR Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 955 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.7980 chunk 171 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 109 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.147637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.125993 restraints weight = 48482.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.126578 restraints weight = 29748.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.127633 restraints weight = 22989.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.127775 restraints weight = 16308.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.128007 restraints weight = 15461.360| |-----------------------------------------------------------------------------| r_work (final): 0.4599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15682 Z= 0.150 Angle : 0.701 12.317 21205 Z= 0.357 Chirality : 0.044 0.240 2279 Planarity : 0.009 0.382 2742 Dihedral : 5.464 47.597 2036 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.41 % Allowed : 21.32 % Favored : 73.27 % 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: -0.25 (0.19), residues: 1859 helix: 0.52 (0.16), residues: 875 sheet: -0.19 (0.27), residues: 339 loop : -0.95 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG B 62 TYR 0.021 0.002 TYR B 149 PHE 0.061 0.002 PHE A 715 TRP 0.009 0.001 TRP B 199 HIS 0.012 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00333 (15681) covalent geometry : angle 0.70132 (21205) hydrogen bonds : bond 0.04847 ( 765) hydrogen bonds : angle 5.41922 ( 2247) Misc. bond : bond 0.01218 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 175 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6717 (mm) REVERT: A 444 TYR cc_start: 0.4937 (OUTLIER) cc_final: 0.4464 (m-80) REVERT: A 462 ASP cc_start: 0.8765 (m-30) cc_final: 0.8465 (t0) REVERT: A 556 MET cc_start: 0.6370 (tpp) cc_final: 0.6080 (tpt) REVERT: A 620 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7199 (mt) REVERT: A 637 LYS cc_start: 0.3057 (OUTLIER) cc_final: 0.2736 (ptmt) REVERT: A 915 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: A 997 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: A 1005 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6789 (m-80) REVERT: B 113 MET cc_start: 0.1269 (ttt) cc_final: 0.0723 (ttt) REVERT: B 119 LYS cc_start: 0.7654 (tppt) cc_final: 0.6915 (mmmt) REVERT: B 227 GLU cc_start: -0.1886 (OUTLIER) cc_final: -0.2660 (tp30) REVERT: B 240 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7148 (mt-10) REVERT: B 279 GLU cc_start: 0.6714 (tp30) cc_final: 0.6255 (tp30) REVERT: B 291 HIS cc_start: 0.5782 (OUTLIER) cc_final: 0.4868 (t70) REVERT: B 307 ILE cc_start: 0.4534 (OUTLIER) cc_final: 0.3753 (tp) REVERT: B 386 HIS cc_start: 0.6619 (OUTLIER) cc_final: 0.6213 (m90) REVERT: B 425 LYS cc_start: 0.7900 (mmtp) cc_final: 0.7612 (mmmt) REVERT: B 454 TYR cc_start: 0.7168 (m-10) cc_final: 0.6947 (m-10) REVERT: B 521 LYS cc_start: 0.6015 (OUTLIER) cc_final: 0.5362 (pttm) REVERT: B 574 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8142 (mt) REVERT: B 589 HIS cc_start: 0.6074 (OUTLIER) cc_final: 0.5638 (m90) REVERT: B 687 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6465 (tmt170) REVERT: B 706 ASP cc_start: 0.7461 (p0) cc_final: 0.6762 (p0) REVERT: B 858 TYR cc_start: 0.6400 (t80) cc_final: 0.6084 (t80) outliers start: 90 outliers final: 64 residues processed: 244 average time/residue: 0.1017 time to fit residues: 38.3525 Evaluate side-chains 238 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 159 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 589 HIS Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 637 LYS Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 715 PHE Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 955 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 124 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 43 optimal weight: 30.0000 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.145594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.123055 restraints weight = 48424.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.123197 restraints weight = 27741.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.124258 restraints weight = 23003.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.124226 restraints weight = 17285.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.124501 restraints weight = 15505.029| |-----------------------------------------------------------------------------| r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15682 Z= 0.188 Angle : 0.737 12.079 21205 Z= 0.376 Chirality : 0.046 0.210 2279 Planarity : 0.005 0.056 2742 Dihedral : 6.726 175.219 2036 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.93 % Favored : 96.02 % Rotamer: Outliers : 5.95 % Allowed : 21.02 % Favored : 73.03 % 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: -0.44 (0.19), residues: 1859 helix: 0.36 (0.16), residues: 877 sheet: -0.35 (0.27), residues: 350 loop : -1.01 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 62 TYR 0.022 0.002 TYR A 779 PHE 0.051 0.002 PHE A 715 TRP 0.014 0.002 TRP B 908 HIS 0.006 0.001 HIS B 589 Details of bonding type rmsd covalent geometry : bond 0.00428 (15681) covalent geometry : angle 0.73743 (21205) hydrogen bonds : bond 0.05120 ( 765) hydrogen bonds : angle 5.56146 ( 2247) Misc. bond : bond 0.00925 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 165 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6636 (mm) REVERT: A 462 ASP cc_start: 0.8989 (m-30) cc_final: 0.8629 (t0) REVERT: A 556 MET cc_start: 0.6511 (tpp) cc_final: 0.6224 (tpt) REVERT: A 566 LYS cc_start: 0.5441 (OUTLIER) cc_final: 0.5011 (ptpt) REVERT: A 620 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7215 (mt) REVERT: A 637 LYS cc_start: 0.2999 (OUTLIER) cc_final: 0.2675 (ptmt) REVERT: A 915 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: A 997 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: A 1005 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6715 (m-80) REVERT: B 113 MET cc_start: 0.1316 (ttt) cc_final: 0.0507 (mmm) REVERT: B 227 GLU cc_start: -0.1915 (OUTLIER) cc_final: -0.2673 (tp30) REVERT: B 240 GLU cc_start: 0.7586 (mm-30) cc_final: 0.6987 (mt-10) REVERT: B 279 GLU cc_start: 0.6963 (tp30) cc_final: 0.6483 (tp30) REVERT: B 291 HIS cc_start: 0.5909 (OUTLIER) cc_final: 0.4993 (t70) REVERT: B 307 ILE cc_start: 0.4785 (OUTLIER) cc_final: 0.4048 (tp) REVERT: B 386 HIS cc_start: 0.6800 (OUTLIER) cc_final: 0.6407 (m90) REVERT: B 521 LYS cc_start: 0.6079 (OUTLIER) cc_final: 0.5485 (pttm) REVERT: B 574 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8150 (mt) REVERT: B 589 HIS cc_start: 0.6297 (OUTLIER) cc_final: 0.5603 (m90) REVERT: B 687 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6446 (tmt170) REVERT: B 706 ASP cc_start: 0.7580 (p0) cc_final: 0.6898 (p0) REVERT: B 858 TYR cc_start: 0.6555 (t80) cc_final: 0.6181 (t80) REVERT: B 915 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7041 (mt0) outliers start: 99 outliers final: 71 residues processed: 245 average time/residue: 0.1007 time to fit residues: 38.8984 Evaluate side-chains 239 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 152 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 589 HIS Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 637 LYS Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 715 PHE Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 955 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 70 optimal weight: 0.3980 chunk 112 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 ASN ** B 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.146083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.124030 restraints weight = 49122.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.124057 restraints weight = 29661.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.125271 restraints weight = 23289.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.125676 restraints weight = 16917.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.125907 restraints weight = 15932.624| |-----------------------------------------------------------------------------| r_work (final): 0.4591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.6459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15682 Z= 0.167 Angle : 0.731 12.862 21205 Z= 0.371 Chirality : 0.045 0.207 2279 Planarity : 0.008 0.322 2742 Dihedral : 6.247 138.655 2036 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 5.53 % Allowed : 21.50 % Favored : 72.97 % 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: -0.45 (0.19), residues: 1859 helix: 0.38 (0.16), residues: 875 sheet: -0.37 (0.27), residues: 350 loop : -1.04 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 62 TYR 0.019 0.002 TYR A 779 PHE 0.051 0.002 PHE A 715 TRP 0.011 0.002 TRP B 908 HIS 0.005 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00375 (15681) covalent geometry : angle 0.73058 (21205) hydrogen bonds : bond 0.04971 ( 765) hydrogen bonds : angle 5.50791 ( 2247) Misc. bond : bond 0.01106 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 160 time to evaluate : 0.461 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 385 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6627 (mm) REVERT: A 462 ASP cc_start: 0.8684 (m-30) cc_final: 0.8400 (t0) REVERT: A 556 MET cc_start: 0.6625 (tpp) cc_final: 0.6400 (tpt) REVERT: A 566 LYS cc_start: 0.5276 (OUTLIER) cc_final: 0.4850 (ptpt) REVERT: A 620 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7059 (mt) REVERT: A 637 LYS cc_start: 0.3312 (OUTLIER) cc_final: 0.2938 (ptmt) REVERT: A 915 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: A 1005 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: B 113 MET cc_start: 0.1333 (ttt) cc_final: 0.0445 (mmm) REVERT: B 227 GLU cc_start: -0.1884 (OUTLIER) cc_final: -0.2674 (tp30) REVERT: B 240 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7128 (mt-10) REVERT: B 244 PHE cc_start: 0.6630 (m-10) cc_final: 0.5597 (t80) REVERT: B 279 GLU cc_start: 0.6806 (tp30) cc_final: 0.6298 (tp30) REVERT: B 291 HIS cc_start: 0.5980 (OUTLIER) cc_final: 0.4633 (t70) REVERT: B 307 ILE cc_start: 0.4637 (OUTLIER) cc_final: 0.3857 (tp) REVERT: B 386 HIS cc_start: 0.6436 (OUTLIER) cc_final: 0.6009 (m90) REVERT: B 425 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7605 (mmtp) REVERT: B 521 LYS cc_start: 0.5993 (OUTLIER) cc_final: 0.5370 (pttm) REVERT: B 574 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8059 (mt) REVERT: B 589 HIS cc_start: 0.6257 (OUTLIER) cc_final: 0.5643 (m90) REVERT: B 687 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6485 (tmt170) REVERT: B 706 ASP cc_start: 0.7425 (p0) cc_final: 0.6720 (p0) REVERT: B 858 TYR cc_start: 0.6135 (t80) cc_final: 0.5881 (t80) outliers start: 92 outliers final: 69 residues processed: 232 average time/residue: 0.1020 time to fit residues: 36.8936 Evaluate side-chains 239 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 155 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 589 HIS Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 637 LYS Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 715 PHE Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 955 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 175 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 120 optimal weight: 0.0040 overall best weight: 2.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.146203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.124158 restraints weight = 48490.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.124639 restraints weight = 29243.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.125312 restraints weight = 25412.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.125536 restraints weight = 18233.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.125892 restraints weight = 16303.790| |-----------------------------------------------------------------------------| r_work (final): 0.4592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.6559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15682 Z= 0.163 Angle : 0.736 12.742 21205 Z= 0.373 Chirality : 0.045 0.229 2279 Planarity : 0.007 0.241 2742 Dihedral : 5.484 46.580 2036 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.87 % Favored : 96.07 % Rotamer: Outliers : 5.11 % Allowed : 21.92 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.45 (0.19), residues: 1859 helix: 0.40 (0.16), residues: 874 sheet: -0.39 (0.27), residues: 349 loop : -1.07 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG B 62 TYR 0.019 0.002 TYR A 779 PHE 0.048 0.002 PHE A 715 TRP 0.011 0.001 TRP B 908 HIS 0.005 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00369 (15681) covalent geometry : angle 0.73623 (21205) hydrogen bonds : bond 0.04907 ( 765) hydrogen bonds : angle 5.48120 ( 2247) Misc. bond : bond 0.00706 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2678.65 seconds wall clock time: 47 minutes 9.55 seconds (2829.55 seconds total)