Starting phenix.real_space_refine on Tue Dec 31 09:54:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzh_24760/12_2024/7rzh_24760.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzh_24760/12_2024/7rzh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rzh_24760/12_2024/7rzh_24760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzh_24760/12_2024/7rzh_24760.map" model { file = "/net/cci-nas-00/data/ceres_data/7rzh_24760/12_2024/7rzh_24760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzh_24760/12_2024/7rzh_24760.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 8.81, per 1000 atoms: 0.58 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: 3.78 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.92 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: 6.22 Time building geometry restraints manager: 4.41 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.740 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.080 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.170 ------------------------------------------------------------------------------- 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 15681 Z= 0.805 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (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 TRP 0.012 0.002 TRP B 560 HIS 0.011 0.001 HIS B 93 PHE 0.020 0.002 PHE B 130 TYR 0.014 0.002 TYR B 779 ARG 0.005 0.001 ARG B 402 *********************** 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 : 1.868 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: 0.4873 (m) REVERT: A 371 MET cc_start: 0.2235 (mmm) cc_final: 0.1883 (mmm) REVERT: A 385 LEU cc_start: 0.7020 (mm) cc_final: 0.6786 (mm) REVERT: A 672 ASN cc_start: 0.7436 (t0) cc_final: 0.7127 (t0) REVERT: A 963 MET cc_start: 0.3184 (ttm) cc_final: 0.2827 (tmm) REVERT: B 61 LYS cc_start: 0.3613 (OUTLIER) cc_final: 0.3041 (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: 0.5953 (t80) REVERT: B 279 GLU cc_start: 0.5509 (tp30) cc_final: 0.5277 (tp30) REVERT: B 307 ILE cc_start: 0.4184 (mt) cc_final: 0.3552 (tt) REVERT: B 687 ARG cc_start: 0.7101 (ptp-170) cc_final: 0.6634 (tmt-80) REVERT: B 706 ASP cc_start: 0.6694 (p0) cc_final: 0.6254 (p0) outliers start: 88 outliers final: 13 residues processed: 501 average time/residue: 0.2846 time to fit residues: 207.8406 Evaluate side-chains 250 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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 157 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 145 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 168 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 300 GLN A 340 HIS A 534 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 573 ASN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 GLN B 922 ASN B 993 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15681 Z= 0.226 Angle : 0.725 14.821 21205 Z= 0.375 Chirality : 0.046 0.235 2279 Planarity : 0.005 0.101 2742 Dihedral : 5.428 47.696 2057 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.78 % Allowed : 16.28 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.19), residues: 1859 helix: 1.74 (0.16), residues: 895 sheet: 1.58 (0.27), residues: 351 loop : -0.19 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 513 HIS 0.008 0.001 HIS B 340 PHE 0.053 0.003 PHE A 715 TYR 0.029 0.002 TYR A 500 ARG 0.009 0.001 ARG A 711 *********************** 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 317 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 254 time to evaluate : 1.862 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 385 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6632 (mm) REVERT: A 943 MET cc_start: 0.3544 (mmt) cc_final: 0.3156 (mmt) REVERT: A 963 MET cc_start: 0.3592 (ttm) cc_final: 0.3155 (tmm) REVERT: B 102 ASN cc_start: 0.6094 (p0) cc_final: 0.5083 (p0) REVERT: B 199 TRP cc_start: 0.5837 (t-100) cc_final: 0.5488 (t-100) REVERT: B 227 GLU cc_start: -0.1680 (OUTLIER) cc_final: -0.2509 (tp30) REVERT: B 240 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7465 (mt-10) REVERT: B 279 GLU cc_start: 0.5739 (tp30) cc_final: 0.5274 (tp30) REVERT: B 307 ILE cc_start: 0.4367 (mt) cc_final: 0.3727 (tt) REVERT: B 337 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6996 (tp) REVERT: B 688 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.5406 (tp) REVERT: B 1011 HIS cc_start: 0.3804 (OUTLIER) cc_final: 0.3529 (t-170) outliers start: 63 outliers final: 27 residues processed: 295 average time/residue: 0.2755 time to fit residues: 124.0112 Evaluate side-chains 234 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 1.841 ------------------------------------------------------------------------------- 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 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 886 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 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 93 optimal weight: 0.0870 chunk 52 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 167 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 196 ASN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN B 672 ASN B 796 GLN ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5780 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15681 Z= 0.200 Angle : 0.655 10.754 21205 Z= 0.339 Chirality : 0.044 0.186 2279 Planarity : 0.005 0.158 2742 Dihedral : 5.041 46.095 2045 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.60 % Allowed : 18.32 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.19), residues: 1859 helix: 1.39 (0.17), residues: 894 sheet: 1.18 (0.27), residues: 346 loop : -0.26 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 409 HIS 0.006 0.001 HIS A 885 PHE 0.050 0.002 PHE A 715 TYR 0.024 0.002 TYR A 666 ARG 0.007 0.000 ARG A 839 *********************** 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 275 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 215 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.2087 (mmm) cc_final: 0.1726 (mmm) REVERT: A 793 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7683 (pt) REVERT: A 943 MET cc_start: 0.3782 (mmt) cc_final: 0.3454 (mmt) REVERT: A 963 MET cc_start: 0.3735 (ttm) cc_final: 0.3333 (tmm) REVERT: B 102 ASN cc_start: 0.6292 (p0) cc_final: 0.5106 (p0) REVERT: B 119 LYS cc_start: 0.7867 (tptt) cc_final: 0.7457 (mmmt) REVERT: B 199 TRP cc_start: 0.5822 (t-100) cc_final: 0.5497 (t-100) REVERT: B 227 GLU cc_start: -0.1986 (OUTLIER) cc_final: -0.2772 (tp30) REVERT: B 240 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7501 (mt-10) REVERT: B 279 GLU cc_start: 0.5737 (tp30) cc_final: 0.5307 (tp30) REVERT: B 307 ILE cc_start: 0.4464 (mt) cc_final: 0.3871 (tt) REVERT: B 324 LYS cc_start: 0.6070 (OUTLIER) cc_final: 0.4752 (ptpt) REVERT: B 688 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.5300 (tp) REVERT: B 706 ASP cc_start: 0.6633 (p0) cc_final: 0.6289 (p0) REVERT: B 1011 HIS cc_start: 0.4124 (OUTLIER) cc_final: 0.3663 (t-170) outliers start: 60 outliers final: 30 residues processed: 256 average time/residue: 0.2769 time to fit residues: 110.1387 Evaluate side-chains 215 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 1.879 ------------------------------------------------------------------------------- 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 278 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 417 LEU 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 642 LEU Chi-restraints excluded: chain A residue 764 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 923 THR Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 54 ILE 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 297 HIS Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 850 ILE 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 167 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 18 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 88 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 573 ASN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN B 232 GLN B 796 GLN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15681 Z= 0.206 Angle : 0.639 11.248 21205 Z= 0.327 Chirality : 0.043 0.248 2279 Planarity : 0.006 0.193 2742 Dihedral : 5.092 47.391 2043 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.02 % Allowed : 18.26 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 1859 helix: 1.30 (0.17), residues: 898 sheet: 0.90 (0.27), residues: 346 loop : -0.33 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 199 HIS 0.006 0.001 HIS A 885 PHE 0.042 0.002 PHE A 715 TYR 0.018 0.002 TYR A 779 ARG 0.012 0.001 ARG B 62 *********************** 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 267 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 200 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 793 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7731 (pt) REVERT: A 943 MET cc_start: 0.3811 (mmt) cc_final: 0.3562 (mmt) REVERT: A 963 MET cc_start: 0.3837 (ttm) cc_final: 0.3449 (ptm) REVERT: B 102 ASN cc_start: 0.6281 (p0) cc_final: 0.5028 (p0) REVERT: B 119 LYS cc_start: 0.7779 (tptt) cc_final: 0.7415 (mmmt) REVERT: B 199 TRP cc_start: 0.5750 (t-100) cc_final: 0.5397 (t-100) REVERT: B 227 GLU cc_start: -0.2081 (OUTLIER) cc_final: -0.2829 (tp30) REVERT: B 240 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7457 (mt-10) REVERT: B 279 GLU cc_start: 0.5841 (tp30) cc_final: 0.5423 (tp30) REVERT: B 307 ILE cc_start: 0.4356 (mt) cc_final: 0.3717 (tt) REVERT: B 308 LYS cc_start: 0.1580 (OUTLIER) cc_final: 0.1188 (pttm) REVERT: B 324 LYS cc_start: 0.6548 (OUTLIER) cc_final: 0.5175 (ptpt) REVERT: B 337 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7307 (tp) REVERT: B 688 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.5046 (tp) REVERT: B 706 ASP cc_start: 0.6722 (p0) cc_final: 0.6354 (p0) REVERT: B 799 MET cc_start: 0.8179 (tmm) cc_final: 0.7868 (ttp) REVERT: B 806 MET cc_start: 0.5766 (mmp) cc_final: 0.5559 (mmt) REVERT: B 908 TRP cc_start: 0.4343 (t-100) cc_final: 0.3501 (t60) REVERT: B 1011 HIS cc_start: 0.4112 (OUTLIER) cc_final: 0.3785 (t-170) outliers start: 67 outliers final: 38 residues processed: 247 average time/residue: 0.2437 time to fit residues: 93.8071 Evaluate side-chains 224 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 179 time to evaluate : 1.886 ------------------------------------------------------------------------------- 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 116 LEU Chi-restraints excluded: chain A residue 194 VAL 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 417 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 764 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 923 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 57 SER 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 308 LYS 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 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 729 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 850 ILE 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 Chi-restraints excluded: chain B residue 1011 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 45 optimal weight: 0.0270 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 GLN A 672 ASN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 HIS ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15681 Z= 0.304 Angle : 0.743 11.949 21205 Z= 0.388 Chirality : 0.047 0.218 2279 Planarity : 0.007 0.204 2742 Dihedral : 5.447 51.599 2041 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.38 % Allowed : 18.62 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.18), residues: 1859 helix: 0.70 (0.16), residues: 889 sheet: 0.57 (0.27), residues: 338 loop : -0.53 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 355 HIS 0.011 0.002 HIS A 885 PHE 0.042 0.003 PHE A 715 TYR 0.048 0.003 TYR A 779 ARG 0.020 0.001 ARG B 62 *********************** 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 264 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 191 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.6571 (tpt90) REVERT: A 943 MET cc_start: 0.4358 (mmt) cc_final: 0.3868 (mmt) REVERT: B 61 LYS cc_start: 0.4630 (OUTLIER) cc_final: 0.3923 (tmtt) REVERT: B 102 ASN cc_start: 0.6504 (p0) cc_final: 0.6003 (p0) REVERT: B 119 LYS cc_start: 0.7980 (tptt) cc_final: 0.7434 (mmmt) REVERT: B 199 TRP cc_start: 0.5726 (t-100) cc_final: 0.5267 (t-100) REVERT: B 227 GLU cc_start: -0.1696 (OUTLIER) cc_final: -0.2639 (tp30) REVERT: B 240 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7384 (mt-10) REVERT: B 279 GLU cc_start: 0.6057 (tp30) cc_final: 0.5556 (tp30) REVERT: B 307 ILE cc_start: 0.4306 (mt) cc_final: 0.3710 (tp) REVERT: B 324 LYS cc_start: 0.6780 (OUTLIER) cc_final: 0.6463 (pttm) REVERT: B 337 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7375 (tp) REVERT: B 574 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7931 (mt) REVERT: B 706 ASP cc_start: 0.6978 (p0) cc_final: 0.6702 (p0) outliers start: 73 outliers final: 45 residues processed: 243 average time/residue: 0.2667 time to fit residues: 99.0425 Evaluate side-chains 222 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 194 VAL 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 387 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 764 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 1004 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 61 LYS 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 227 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 475 ASN Chi-restraints excluded: chain B residue 574 LEU 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 688 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 105 optimal weight: 0.0060 chunk 44 optimal weight: 20.0000 chunk 179 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 800 GLN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 HIS B 184 ASN B 332 HIS ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15681 Z= 0.198 Angle : 0.647 10.304 21205 Z= 0.332 Chirality : 0.043 0.218 2279 Planarity : 0.007 0.279 2742 Dihedral : 5.302 50.044 2041 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.32 % Allowed : 19.28 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1859 helix: 0.80 (0.16), residues: 893 sheet: 0.44 (0.28), residues: 338 loop : -0.46 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 908 HIS 0.010 0.001 HIS A 885 PHE 0.041 0.002 PHE A 715 TYR 0.033 0.002 TYR A 779 ARG 0.009 0.001 ARG B 62 *********************** 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 261 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 189 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.3779 (pmm) cc_final: 0.2332 (mmp) REVERT: A 451 THR cc_start: 0.5162 (p) cc_final: 0.4896 (p) REVERT: A 793 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7609 (pt) REVERT: B 61 LYS cc_start: 0.4426 (OUTLIER) cc_final: 0.3909 (tmtt) REVERT: B 102 ASN cc_start: 0.6554 (p0) cc_final: 0.6051 (p0) REVERT: B 119 LYS cc_start: 0.7930 (tptt) cc_final: 0.7355 (mmmt) REVERT: B 199 TRP cc_start: 0.5740 (t-100) cc_final: 0.5320 (t-100) REVERT: B 227 GLU cc_start: -0.1724 (OUTLIER) cc_final: -0.2671 (tp30) REVERT: B 240 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7372 (mt-10) REVERT: B 279 GLU cc_start: 0.6047 (tp30) cc_final: 0.5578 (tp30) REVERT: B 307 ILE cc_start: 0.4294 (mt) cc_final: 0.3701 (tp) REVERT: B 324 LYS cc_start: 0.6745 (OUTLIER) cc_final: 0.6418 (pttm) REVERT: B 337 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7486 (tp) REVERT: B 574 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8057 (mt) REVERT: B 687 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.6457 (tmt170) REVERT: B 688 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.5217 (tp) REVERT: B 706 ASP cc_start: 0.6727 (p0) cc_final: 0.6450 (p0) outliers start: 72 outliers final: 46 residues processed: 242 average time/residue: 0.2676 time to fit residues: 100.8182 Evaluate side-chains 224 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 116 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 384 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 478 VAL 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 684 TYR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 774 ARG 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 954 VAL Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 227 GLU 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 475 ASN Chi-restraints excluded: chain B residue 574 LEU 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 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 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 173 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 131 optimal weight: 0.1980 chunk 101 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 GLN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 HIS ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15681 Z= 0.195 Angle : 0.653 11.334 21205 Z= 0.335 Chirality : 0.043 0.195 2279 Planarity : 0.008 0.382 2742 Dihedral : 5.292 50.408 2041 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.08 % Allowed : 20.42 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 1859 helix: 0.86 (0.16), residues: 887 sheet: 0.35 (0.28), residues: 343 loop : -0.45 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 908 HIS 0.007 0.001 HIS A 885 PHE 0.047 0.002 PHE A 715 TYR 0.030 0.002 TYR A 779 ARG 0.012 0.001 ARG B 62 *********************** 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 253 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 185 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.3766 (pmm) cc_final: 0.2446 (mmp) REVERT: A 451 THR cc_start: 0.5200 (p) cc_final: 0.4912 (p) REVERT: A 494 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.5856 (pp20) REVERT: A 793 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7609 (pt) REVERT: B 61 LYS cc_start: 0.4398 (OUTLIER) cc_final: 0.4192 (tmtt) REVERT: B 102 ASN cc_start: 0.6602 (p0) cc_final: 0.6114 (p0) REVERT: B 119 LYS cc_start: 0.7850 (tptt) cc_final: 0.7314 (mmmt) REVERT: B 199 TRP cc_start: 0.5760 (t-100) cc_final: 0.5360 (t-100) REVERT: B 227 GLU cc_start: -0.1566 (OUTLIER) cc_final: -0.2554 (tp30) REVERT: B 240 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7446 (mt-10) REVERT: B 279 GLU cc_start: 0.6066 (tp30) cc_final: 0.5585 (tp30) REVERT: B 291 HIS cc_start: 0.5406 (p-80) cc_final: 0.4401 (t70) REVERT: B 307 ILE cc_start: 0.4278 (mt) cc_final: 0.3688 (tp) REVERT: B 324 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.5663 (ptpt) REVERT: B 337 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7498 (tp) REVERT: B 687 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.6464 (tmt170) REVERT: B 688 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.5452 (tp) REVERT: B 706 ASP cc_start: 0.6826 (p0) cc_final: 0.6513 (p0) outliers start: 68 outliers final: 48 residues processed: 236 average time/residue: 0.2604 time to fit residues: 95.5233 Evaluate side-chains 234 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 178 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 116 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 384 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 531 ILE 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 758 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 774 ARG 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 954 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 227 GLU 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 434 THR 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 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 923 THR Chi-restraints excluded: chain B residue 928 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 110 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 16 optimal weight: 30.0000 chunk 140 optimal weight: 8.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN B 112 HIS ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS B 672 ASN B 796 GLN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15681 Z= 0.167 Angle : 0.630 12.253 21205 Z= 0.319 Chirality : 0.042 0.185 2279 Planarity : 0.010 0.484 2742 Dihedral : 5.502 98.647 2041 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.96 % Allowed : 20.78 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 1859 helix: 1.05 (0.17), residues: 882 sheet: 0.44 (0.28), residues: 340 loop : -0.46 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 908 HIS 0.011 0.001 HIS B 112 PHE 0.047 0.002 PHE A 715 TYR 0.029 0.001 TYR A 779 ARG 0.013 0.000 ARG B 62 *********************** 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 255 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 189 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LEU cc_start: 0.3855 (OUTLIER) cc_final: 0.3182 (tp) REVERT: A 195 MET cc_start: 0.3440 (pmm) cc_final: 0.2479 (mmp) REVERT: A 451 THR cc_start: 0.4929 (p) cc_final: 0.4490 (p) REVERT: A 494 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6573 (pt0) REVERT: A 793 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7539 (pt) REVERT: B 102 ASN cc_start: 0.6648 (p0) cc_final: 0.6214 (p0) REVERT: B 119 LYS cc_start: 0.7722 (tptt) cc_final: 0.7282 (tppt) REVERT: B 199 TRP cc_start: 0.5663 (t-100) cc_final: 0.5305 (t-100) REVERT: B 227 GLU cc_start: -0.2025 (OUTLIER) cc_final: -0.2570 (tp30) REVERT: B 240 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7482 (mt-10) REVERT: B 279 GLU cc_start: 0.6043 (tp30) cc_final: 0.5554 (tp30) REVERT: B 291 HIS cc_start: 0.5324 (p-80) cc_final: 0.4330 (t70) REVERT: B 307 ILE cc_start: 0.4453 (mt) cc_final: 0.3832 (tp) REVERT: B 324 LYS cc_start: 0.6812 (OUTLIER) cc_final: 0.5465 (ptpt) REVERT: B 688 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.5270 (tp) REVERT: B 706 ASP cc_start: 0.6583 (p0) cc_final: 0.6284 (p0) outliers start: 66 outliers final: 47 residues processed: 239 average time/residue: 0.2637 time to fit residues: 97.2775 Evaluate side-chains 230 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 177 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 173 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 384 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 531 ILE 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 758 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 802 THR 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 963 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 54 ILE 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 227 GLU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 434 THR 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 688 LEU Chi-restraints excluded: chain B residue 715 PHE 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 923 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 163 optimal weight: 0.9990 chunk 171 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 805 ASN ** 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.5837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15681 Z= 0.276 Angle : 0.730 12.222 21205 Z= 0.372 Chirality : 0.045 0.196 2279 Planarity : 0.006 0.153 2742 Dihedral : 6.513 162.530 2041 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.14 % Allowed : 20.66 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 1859 helix: 0.69 (0.16), residues: 879 sheet: 0.12 (0.27), residues: 360 loop : -0.61 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 908 HIS 0.012 0.002 HIS B 112 PHE 0.055 0.002 PHE A 715 TYR 0.027 0.002 TYR A 779 ARG 0.017 0.001 ARG B 62 *********************** 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 245 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 176 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LEU cc_start: 0.3380 (OUTLIER) cc_final: 0.2701 (tp) REVERT: A 195 MET cc_start: 0.3485 (pmm) cc_final: 0.2312 (mmp) REVERT: B 102 ASN cc_start: 0.6316 (p0) cc_final: 0.5853 (p0) REVERT: B 112 HIS cc_start: 0.4438 (OUTLIER) cc_final: 0.4186 (t70) REVERT: B 119 LYS cc_start: 0.7883 (tptt) cc_final: 0.7385 (tppt) REVERT: B 227 GLU cc_start: -0.1807 (OUTLIER) cc_final: -0.2539 (tp30) REVERT: B 240 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7467 (mt-10) REVERT: B 291 HIS cc_start: 0.5613 (p-80) cc_final: 0.4670 (t70) REVERT: B 324 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.5740 (ptpt) REVERT: B 706 ASP cc_start: 0.6845 (p0) cc_final: 0.6546 (p0) outliers start: 69 outliers final: 50 residues processed: 225 average time/residue: 0.2660 time to fit residues: 92.0101 Evaluate side-chains 218 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 173 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 384 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 478 VAL 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 764 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 774 ARG 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 1004 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 112 HIS 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 324 LYS Chi-restraints excluded: chain B residue 333 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 377 VAL 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 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 688 LEU Chi-restraints excluded: chain B residue 715 PHE 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 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 109 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 83 optimal weight: 0.3980 chunk 122 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 113 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 GLN ** A 805 ASN ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15681 Z= 0.257 Angle : 0.739 13.096 21205 Z= 0.376 Chirality : 0.045 0.192 2279 Planarity : 0.006 0.170 2742 Dihedral : 6.549 160.696 2041 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.54 % Allowed : 21.14 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.19), residues: 1859 helix: 0.58 (0.16), residues: 879 sheet: 0.05 (0.27), residues: 360 loop : -0.70 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 908 HIS 0.055 0.002 HIS B 112 PHE 0.059 0.002 PHE A 715 TYR 0.027 0.002 TYR A 779 ARG 0.020 0.001 ARG B 62 ********************** 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 229 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LEU cc_start: 0.3423 (OUTLIER) cc_final: 0.2756 (tp) REVERT: A 195 MET cc_start: 0.3349 (pmm) cc_final: 0.2107 (mmp) REVERT: A 806 MET cc_start: 0.7058 (mmm) cc_final: 0.6484 (mmt) REVERT: B 119 LYS cc_start: 0.7902 (tptt) cc_final: 0.7418 (tppt) REVERT: B 227 GLU cc_start: -0.1861 (OUTLIER) cc_final: -0.2697 (tp30) REVERT: B 240 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7469 (mt-10) REVERT: B 324 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.5597 (ptpt) REVERT: B 706 ASP cc_start: 0.6721 (p0) cc_final: 0.6404 (p0) REVERT: B 915 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7184 (mt0) outliers start: 59 outliers final: 50 residues processed: 217 average time/residue: 0.2497 time to fit residues: 84.4701 Evaluate side-chains 215 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 173 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 384 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 417 LEU 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 764 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 774 ARG 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 54 ILE Chi-restraints excluded: chain B residue 99 ASP 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 295 GLU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 377 VAL 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 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 688 LEU Chi-restraints excluded: chain B residue 715 PHE 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 117 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 294 GLN A 672 ASN A 805 ASN A 952 HIS ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.149352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.127378 restraints weight = 47948.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.126317 restraints weight = 32194.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.127362 restraints weight = 26178.232| |-----------------------------------------------------------------------------| r_work (final): 0.4608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.6090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 15681 Z= 0.203 Angle : 0.703 14.994 21205 Z= 0.354 Chirality : 0.043 0.200 2279 Planarity : 0.009 0.416 2742 Dihedral : 5.485 57.212 2041 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.36 % Allowed : 21.50 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 1859 helix: 0.72 (0.17), residues: 879 sheet: 0.11 (0.27), residues: 357 loop : -0.73 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 908 HIS 0.006 0.001 HIS A 885 PHE 0.059 0.002 PHE A 715 TYR 0.028 0.002 TYR A 779 ARG 0.026 0.001 ARG B 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3219.22 seconds wall clock time: 59 minutes 47.04 seconds (3587.04 seconds total)