Starting phenix.real_space_refine on Sun Aug 24 17:36:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fw2_29496/08_2025/8fw2_29496_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fw2_29496/08_2025/8fw2_29496.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/8fw2_29496/08_2025/8fw2_29496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fw2_29496/08_2025/8fw2_29496.map" model { file = "/net/cci-nas-00/data/ceres_data/8fw2_29496/08_2025/8fw2_29496_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fw2_29496/08_2025/8fw2_29496_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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 111 5.16 5 C 13824 2.51 5 N 3660 2.21 5 O 4017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21612 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7204 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Chain: "B" Number of atoms: 7204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7204 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Chain: "C" Number of atoms: 7204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7204 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Time building chain proxies: 4.74, per 1000 atoms: 0.22 Number of scatterers: 21612 At special positions: 0 Unit cell: (216.144, 146.94, 100.488, 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 111 16.00 O 4017 8.00 N 3660 7.00 C 13824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 998.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5130 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 16 sheets defined 50.5% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 95 through 109 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 224 through 228 removed outlier: 3.599A pdb=" N ILE A 227 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 240 removed outlier: 4.175A pdb=" N ALA A 234 " --> pdb=" O GLN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 258 through 267 Processing helix chain 'A' and resid 268 through 271 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 314 through 328 Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 337 through 347 removed outlier: 4.135A pdb=" N THR A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 removed outlier: 3.940A pdb=" N ASN A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 382 through 403 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 418 through 425 Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 463 through 475 Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 487 through 496 Processing helix chain 'A' and resid 499 through 511 Processing helix chain 'A' and resid 541 through 564 Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 592 through 602 removed outlier: 4.169A pdb=" N PHE A 596 " --> pdb=" O PRO A 592 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 609 Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.819A pdb=" N VAL A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 685 Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 725 through 733 Processing helix chain 'A' and resid 778 through 788 Processing helix chain 'A' and resid 808 through 815 removed outlier: 3.586A pdb=" N VAL A 812 " --> pdb=" O MET A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 843 Processing helix chain 'A' and resid 844 through 846 No H-bonds generated for 'chain 'A' and resid 844 through 846' Processing helix chain 'A' and resid 863 through 873 Processing helix chain 'A' and resid 891 through 894 Processing helix chain 'A' and resid 895 through 904 removed outlier: 3.785A pdb=" N HIS A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 931 Processing helix chain 'A' and resid 954 through 958 Processing helix chain 'A' and resid 959 through 964 Processing helix chain 'A' and resid 980 through 992 removed outlier: 3.769A pdb=" N SER A 992 " --> pdb=" O SER A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1015 Processing helix chain 'B' and resid 95 through 109 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 230 through 240 removed outlier: 4.220A pdb=" N ALA B 234 " --> pdb=" O GLN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 267 Processing helix chain 'B' and resid 267 through 272 removed outlier: 4.359A pdb=" N PHE B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 314 through 328 Processing helix chain 'B' and resid 330 through 335 Processing helix chain 'B' and resid 338 through 347 removed outlier: 4.378A pdb=" N THR B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 374 removed outlier: 3.813A pdb=" N ASN B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 378 Processing helix chain 'B' and resid 382 through 404 Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 415 through 417 No H-bonds generated for 'chain 'B' and resid 415 through 417' Processing helix chain 'B' and resid 418 through 425 Processing helix chain 'B' and resid 443 through 460 Processing helix chain 'B' and resid 463 through 475 Processing helix chain 'B' and resid 479 through 484 Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 498 through 511 Processing helix chain 'B' and resid 541 through 564 Processing helix chain 'B' and resid 571 through 580 Processing helix chain 'B' and resid 592 through 602 removed outlier: 4.101A pdb=" N PHE B 596 " --> pdb=" O PRO B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 609 Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.512A pdb=" N VAL B 649 " --> pdb=" O PRO B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 685 Processing helix chain 'B' and resid 703 through 709 Processing helix chain 'B' and resid 725 through 735 Processing helix chain 'B' and resid 778 through 787 Processing helix chain 'B' and resid 788 through 790 No H-bonds generated for 'chain 'B' and resid 788 through 790' Processing helix chain 'B' and resid 808 through 815 removed outlier: 3.618A pdb=" N VAL B 812 " --> pdb=" O MET B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 843 Processing helix chain 'B' and resid 844 through 846 No H-bonds generated for 'chain 'B' and resid 844 through 846' Processing helix chain 'B' and resid 863 through 873 Processing helix chain 'B' and resid 891 through 894 Processing helix chain 'B' and resid 895 through 904 removed outlier: 3.912A pdb=" N HIS B 902 " --> pdb=" O SER B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 931 Processing helix chain 'B' and resid 954 through 958 Processing helix chain 'B' and resid 959 through 964 Processing helix chain 'B' and resid 980 through 992 removed outlier: 3.872A pdb=" N SER B 992 " --> pdb=" O SER B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1015 Processing helix chain 'C' and resid 95 through 109 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 191 through 195 Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 211 through 220 Processing helix chain 'C' and resid 224 through 228 removed outlier: 3.836A pdb=" N ILE C 227 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 249 through 253 Processing helix chain 'C' and resid 254 through 257 Processing helix chain 'C' and resid 258 through 267 Processing helix chain 'C' and resid 280 through 287 removed outlier: 4.838A pdb=" N ARG C 285 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 313 Processing helix chain 'C' and resid 314 through 328 Processing helix chain 'C' and resid 330 through 335 Processing helix chain 'C' and resid 337 through 347 removed outlier: 3.767A pdb=" N CYS C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 374 removed outlier: 3.781A pdb=" N ASN C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 378 Processing helix chain 'C' and resid 382 through 404 Processing helix chain 'C' and resid 409 through 413 Processing helix chain 'C' and resid 415 through 417 No H-bonds generated for 'chain 'C' and resid 415 through 417' Processing helix chain 'C' and resid 418 through 425 Processing helix chain 'C' and resid 443 through 460 Processing helix chain 'C' and resid 463 through 475 Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'C' and resid 487 through 496 Processing helix chain 'C' and resid 498 through 511 Processing helix chain 'C' and resid 529 through 533 Processing helix chain 'C' and resid 541 through 564 Processing helix chain 'C' and resid 573 through 580 removed outlier: 3.956A pdb=" N ALA C 577 " --> pdb=" O GLN C 573 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE C 578 " --> pdb=" O GLU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 removed outlier: 4.157A pdb=" N PHE C 596 " --> pdb=" O PRO C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 609 Processing helix chain 'C' and resid 645 through 653 removed outlier: 3.888A pdb=" N VAL C 649 " --> pdb=" O PRO C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 685 Processing helix chain 'C' and resid 703 through 709 Processing helix chain 'C' and resid 725 through 733 Processing helix chain 'C' and resid 778 through 787 Processing helix chain 'C' and resid 788 through 790 No H-bonds generated for 'chain 'C' and resid 788 through 790' Processing helix chain 'C' and resid 808 through 815 removed outlier: 3.640A pdb=" N VAL C 812 " --> pdb=" O MET C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 843 Processing helix chain 'C' and resid 844 through 846 No H-bonds generated for 'chain 'C' and resid 844 through 846' Processing helix chain 'C' and resid 863 through 873 Processing helix chain 'C' and resid 891 through 894 Processing helix chain 'C' and resid 895 through 904 removed outlier: 3.947A pdb=" N HIS C 902 " --> pdb=" O SER C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 931 Processing helix chain 'C' and resid 954 through 958 Processing helix chain 'C' and resid 959 through 964 Processing helix chain 'C' and resid 980 through 992 removed outlier: 3.829A pdb=" N SER C 992 " --> pdb=" O SER C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1008 through 1015 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 153 removed outlier: 5.084A pdb=" N GLU A 150 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N THR A 294 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N CYS A 165 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N THR A 279 " --> pdb=" O CYS A 165 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 167 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA4, first strand: chain 'A' and resid 583 through 587 removed outlier: 6.428A pdb=" N ARG A 660 " --> pdb=" O SER A 689 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ARG A 691 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU A 662 " --> pdb=" O ARG A 691 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLN A 693 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL A 664 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LYS A 695 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A 666 " --> pdb=" O LYS A 695 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N THR A 688 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N SER A 716 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU A 690 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N MET A 718 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 692 " --> pdb=" O MET A 718 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLU A 720 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE A 694 " --> pdb=" O GLU A 720 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU A 741 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASP A 771 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 743 " --> pdb=" O ASP A 771 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 859 through 860 Processing sheet with id=AA6, first strand: chain 'A' and resid 884 through 885 removed outlier: 6.959A pdb=" N LEU A 884 " --> pdb=" O GLY A 913 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 912 " --> pdb=" O ASN A 943 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 153 removed outlier: 5.096A pdb=" N GLU B 150 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 141 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N THR B 294 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N CYS B 165 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N THR B 279 " --> pdb=" O CYS B 165 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE B 167 " --> pdb=" O THR B 279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB1, first strand: chain 'B' and resid 583 through 587 removed outlier: 6.463A pdb=" N ARG B 660 " --> pdb=" O SER B 689 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ARG B 691 " --> pdb=" O ARG B 660 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU B 662 " --> pdb=" O ARG B 691 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLN B 693 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 664 " --> pdb=" O GLN B 693 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LYS B 695 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 666 " --> pdb=" O LYS B 695 " (cutoff:3.500A) removed outlier: 10.573A pdb=" N THR B 688 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 9.418A pdb=" N SER B 716 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU B 690 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N MET B 718 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B 692 " --> pdb=" O MET B 718 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLU B 720 " --> pdb=" O LEU B 692 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE B 694 " --> pdb=" O GLU B 720 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU B 741 " --> pdb=" O ILE B 769 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASP B 771 " --> pdb=" O LEU B 741 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 743 " --> pdb=" O ASP B 771 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 884 through 885 removed outlier: 7.013A pdb=" N LEU B 884 " --> pdb=" O GLY B 913 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 912 " --> pdb=" O ASN B 943 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AB4, first strand: chain 'C' and resid 148 through 153 removed outlier: 5.160A pdb=" N GLU C 150 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG C 141 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N THR C 294 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS C 165 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR C 279 " --> pdb=" O CYS C 165 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE C 167 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'C' and resid 583 through 587 removed outlier: 6.360A pdb=" N ARG C 660 " --> pdb=" O SER C 689 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ARG C 691 " --> pdb=" O ARG C 660 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU C 662 " --> pdb=" O ARG C 691 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLN C 693 " --> pdb=" O LEU C 662 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 664 " --> pdb=" O GLN C 693 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LYS C 695 " --> pdb=" O VAL C 664 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU C 666 " --> pdb=" O LYS C 695 " (cutoff:3.500A) removed outlier: 10.901A pdb=" N THR C 688 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N SER C 716 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU C 690 " --> pdb=" O SER C 716 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N MET C 718 " --> pdb=" O LEU C 690 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 692 " --> pdb=" O MET C 718 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLU C 720 " --> pdb=" O LEU C 692 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE C 694 " --> pdb=" O GLU C 720 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 884 through 885 removed outlier: 6.908A pdb=" N LEU C 884 " --> pdb=" O GLY C 913 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU C 912 " --> pdb=" O ASN C 943 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 942 " --> pdb=" O PHE C 969 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 942 hydrogen bonds defined for protein. 2589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4224 1.32 - 1.45: 5075 1.45 - 1.57: 12539 1.57 - 1.70: 11 1.70 - 1.82: 162 Bond restraints: 22011 Sorted by residual: bond pdb=" CB ILE C 644 " pdb=" CG1 ILE C 644 " ideal model delta sigma weight residual 1.530 1.605 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CB ILE A 644 " pdb=" CG1 ILE A 644 " ideal model delta sigma weight residual 1.530 1.605 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C ALA A 784 " pdb=" O ALA A 784 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.17e-02 7.31e+03 8.99e+00 bond pdb=" C GLU A 818 " pdb=" N PRO A 819 " ideal model delta sigma weight residual 1.331 1.369 -0.038 1.27e-02 6.20e+03 8.96e+00 bond pdb=" CA ALA A 432 " pdb=" C ALA A 432 " ideal model delta sigma weight residual 1.533 1.517 0.017 5.60e-03 3.19e+04 8.77e+00 ... (remaining 22006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 27528 2.02 - 4.04: 1884 4.04 - 6.06: 210 6.06 - 8.08: 71 8.08 - 10.10: 4 Bond angle restraints: 29697 Sorted by residual: angle pdb=" C GLU B 818 " pdb=" N PRO B 819 " pdb=" CA PRO B 819 " ideal model delta sigma weight residual 119.89 129.64 -9.75 1.02e+00 9.61e-01 9.15e+01 angle pdb=" C VAL A 906 " pdb=" N PRO A 907 " pdb=" CA PRO A 907 " ideal model delta sigma weight residual 119.56 127.51 -7.95 1.02e+00 9.61e-01 6.08e+01 angle pdb=" C LEU C 886 " pdb=" N PRO C 887 " pdb=" CA PRO C 887 " ideal model delta sigma weight residual 119.78 127.77 -7.99 1.03e+00 9.43e-01 6.02e+01 angle pdb=" C LEU B 602 " pdb=" N PRO B 603 " pdb=" CA PRO B 603 " ideal model delta sigma weight residual 120.03 127.49 -7.46 9.90e-01 1.02e+00 5.67e+01 angle pdb=" C THR C 111 " pdb=" N PRO C 112 " pdb=" CA PRO C 112 " ideal model delta sigma weight residual 119.56 127.17 -7.61 1.02e+00 9.61e-01 5.57e+01 ... (remaining 29692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 12768 17.59 - 35.18: 414 35.18 - 52.77: 71 52.77 - 70.37: 54 70.37 - 87.96: 10 Dihedral angle restraints: 13317 sinusoidal: 5427 harmonic: 7890 Sorted by residual: dihedral pdb=" CA SER B 163 " pdb=" C SER B 163 " pdb=" N PRO B 164 " pdb=" CA PRO B 164 " ideal model delta harmonic sigma weight residual -180.00 -145.96 -34.04 0 5.00e+00 4.00e-02 4.64e+01 dihedral pdb=" CA SER A 163 " pdb=" C SER A 163 " pdb=" N PRO A 164 " pdb=" CA PRO A 164 " ideal model delta harmonic sigma weight residual -180.00 -146.07 -33.93 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA SER C 163 " pdb=" C SER C 163 " pdb=" N PRO C 164 " pdb=" CA PRO C 164 " ideal model delta harmonic sigma weight residual -180.00 -146.27 -33.73 0 5.00e+00 4.00e-02 4.55e+01 ... (remaining 13314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2290 0.066 - 0.132: 881 0.132 - 0.198: 238 0.198 - 0.264: 9 0.264 - 0.330: 2 Chirality restraints: 3420 Sorted by residual: chirality pdb=" CB ILE A 644 " pdb=" CA ILE A 644 " pdb=" CG1 ILE A 644 " pdb=" CG2 ILE A 644 " both_signs ideal model delta sigma weight residual False 2.64 2.97 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB ILE C 644 " pdb=" CA ILE C 644 " pdb=" CG1 ILE C 644 " pdb=" CG2 ILE C 644 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CG LEU C 751 " pdb=" CB LEU C 751 " pdb=" CD1 LEU C 751 " pdb=" CD2 LEU C 751 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3417 not shown) Planarity restraints: 3765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 917 " -0.034 2.00e-02 2.50e+03 1.67e-02 6.98e+00 pdb=" CG TRP C 917 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP C 917 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP C 917 " 0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP C 917 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 917 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 917 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 917 " -0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 917 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 917 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 818 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C GLU A 818 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU A 818 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO A 819 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 585 " 0.027 2.00e-02 2.50e+03 1.54e-02 4.77e+00 pdb=" CG TYR C 585 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR C 585 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR C 585 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR C 585 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C 585 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR C 585 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 585 " 0.025 2.00e-02 2.50e+03 ... (remaining 3762 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4223 2.77 - 3.30: 20607 3.30 - 3.83: 33485 3.83 - 4.37: 42489 4.37 - 4.90: 69034 Nonbonded interactions: 169838 Sorted by model distance: nonbonded pdb=" O SER B 481 " pdb=" OG SER B 485 " model vdw 2.235 3.040 nonbonded pdb=" O SER C 481 " pdb=" OG SER C 485 " model vdw 2.375 3.040 nonbonded pdb=" O SER A 481 " pdb=" OG SER A 485 " model vdw 2.379 3.040 nonbonded pdb=" OD1 ASP B 821 " pdb=" NZ LYS B 849 " model vdw 2.379 3.120 nonbonded pdb=" O ALA A 945 " pdb=" OG SER A 973 " model vdw 2.383 3.040 ... (remaining 169833 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 8.650 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.090 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 0.011 0.079 22011 Z= 0.617 Angle : 1.161 10.099 29697 Z= 0.806 Chirality : 0.070 0.330 3420 Planarity : 0.004 0.031 3765 Dihedral : 10.693 87.956 8187 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.74 % Allowed : 5.30 % Favored : 93.96 % Rotamer: Outliers : 0.17 % Allowed : 0.78 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 6.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.16), residues: 2700 helix: -0.10 (0.14), residues: 1140 sheet: 0.28 (0.29), residues: 351 loop : -0.43 (0.19), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.029 0.004 TYR B 449 PHE 0.024 0.003 PHE B 253 TRP 0.034 0.005 TRP C 917 HIS 0.004 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.01127 (22011) covalent geometry : angle 1.16074 (29697) hydrogen bonds : bond 0.18966 ( 942) hydrogen bonds : angle 6.75040 ( 2589) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 593 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8113 (tp30) cc_final: 0.7815 (pt0) REVERT: A 798 LEU cc_start: 0.8239 (tp) cc_final: 0.6928 (tp) REVERT: A 810 TYR cc_start: 0.7462 (m-80) cc_final: 0.7161 (m-80) REVERT: A 907 PRO cc_start: 0.7989 (Cg_exo) cc_final: 0.7669 (Cg_endo) REVERT: B 111 THR cc_start: 0.9363 (m) cc_final: 0.9040 (p) REVERT: B 691 ARG cc_start: 0.6901 (mtt180) cc_final: 0.6659 (mtt-85) REVERT: B 903 LEU cc_start: 0.7928 (mt) cc_final: 0.7662 (tp) REVERT: B 963 ASN cc_start: 0.6677 (m-40) cc_final: 0.6103 (t0) REVERT: B 997 LEU cc_start: 0.8706 (tp) cc_final: 0.8489 (tp) REVERT: C 135 THR cc_start: 0.8432 (p) cc_final: 0.8162 (t) REVERT: C 477 MET cc_start: 0.7885 (mmt) cc_final: 0.7496 (mmt) REVERT: C 547 LYS cc_start: 0.7234 (mttt) cc_final: 0.7011 (mttp) REVERT: C 563 GLN cc_start: 0.8201 (tt0) cc_final: 0.7984 (tt0) REVERT: C 568 LYS cc_start: 0.7851 (mttt) cc_final: 0.7641 (mtmm) REVERT: C 611 PHE cc_start: 0.6233 (m-80) cc_final: 0.5759 (m-10) REVERT: C 875 MET cc_start: 0.5206 (mtt) cc_final: 0.4065 (ppp) REVERT: C 878 LEU cc_start: 0.8270 (tp) cc_final: 0.7772 (mp) REVERT: C 917 TRP cc_start: 0.4607 (p90) cc_final: 0.2432 (p90) REVERT: C 958 MET cc_start: 0.7362 (tpp) cc_final: 0.6816 (tmm) outliers start: 4 outliers final: 2 residues processed: 596 average time/residue: 0.1546 time to fit residues: 137.8757 Evaluate side-chains 277 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 275 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 361 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN A 155 ASN A 241 GLN A 269 HIS A 348 GLN A 364 HIS A 858 ASN B 151 GLN B 348 GLN B 800 HIS B 908 GLN B 916 ASN C 147 HIS C 269 HIS C 273 ASN C 348 GLN C 411 GLN C 587 ASN C 657 GLN C 940 GLN C 943 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.168425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.133391 restraints weight = 39666.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.129075 restraints weight = 56500.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.127079 restraints weight = 42481.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.126841 restraints weight = 41795.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.127204 restraints weight = 38085.163| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22011 Z= 0.177 Angle : 0.715 11.453 29697 Z= 0.376 Chirality : 0.043 0.175 3420 Planarity : 0.005 0.056 3765 Dihedral : 5.049 31.240 2873 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.07 % Favored : 94.78 % Rotamer: Outliers : 2.19 % Allowed : 8.54 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.17), residues: 2700 helix: 0.77 (0.15), residues: 1176 sheet: 0.50 (0.28), residues: 327 loop : -0.77 (0.19), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 288 TYR 0.018 0.002 TYR B 594 PHE 0.027 0.002 PHE A 969 TRP 0.019 0.002 TRP C 917 HIS 0.006 0.001 HIS C 797 Details of bonding type rmsd covalent geometry : bond 0.00400 (22011) covalent geometry : angle 0.71549 (29697) hydrogen bonds : bond 0.04982 ( 942) hydrogen bonds : angle 4.94277 ( 2589) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 332 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 TYR cc_start: 0.7628 (t80) cc_final: 0.7410 (t80) REVERT: A 586 ILE cc_start: 0.8147 (mm) cc_final: 0.7673 (mm) REVERT: A 985 ARG cc_start: 0.5093 (mmt180) cc_final: 0.4242 (mtt180) REVERT: B 111 THR cc_start: 0.9256 (m) cc_final: 0.8816 (p) REVERT: B 258 CYS cc_start: 0.8452 (t) cc_final: 0.8177 (t) REVERT: B 963 ASN cc_start: 0.6813 (m-40) cc_final: 0.6386 (t0) REVERT: B 985 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7892 (mmm-85) REVERT: C 238 LYS cc_start: 0.9061 (tmtt) cc_final: 0.8787 (tmmt) REVERT: C 344 THR cc_start: 0.9160 (t) cc_final: 0.8943 (t) REVERT: C 477 MET cc_start: 0.7594 (mmt) cc_final: 0.6866 (mmt) REVERT: C 562 TYR cc_start: 0.8499 (t80) cc_final: 0.8003 (t80) REVERT: C 838 LYS cc_start: 0.7601 (mmmt) cc_final: 0.7144 (ptpt) REVERT: C 902 HIS cc_start: 0.5543 (OUTLIER) cc_final: 0.4669 (t-170) REVERT: C 917 TRP cc_start: 0.3850 (p90) cc_final: 0.2263 (p90) REVERT: C 963 ASN cc_start: 0.7455 (m-40) cc_final: 0.6903 (t0) outliers start: 53 outliers final: 35 residues processed: 371 average time/residue: 0.1449 time to fit residues: 83.8870 Evaluate side-chains 257 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 835 ASN Chi-restraints excluded: chain C residue 902 HIS Chi-restraints excluded: chain C residue 943 ASN Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 25 optimal weight: 0.6980 chunk 199 optimal weight: 0.7980 chunk 249 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 204 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 134 optimal weight: 0.0060 chunk 192 optimal weight: 0.5980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN A 241 GLN A 269 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 ASN B 155 ASN B 943 ASN ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.168185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.137464 restraints weight = 39267.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.132615 restraints weight = 57207.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130434 restraints weight = 47904.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.130913 restraints weight = 44521.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.130810 restraints weight = 36393.880| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22011 Z= 0.125 Angle : 0.614 8.836 29697 Z= 0.322 Chirality : 0.040 0.156 3420 Planarity : 0.004 0.051 3765 Dihedral : 4.816 30.761 2873 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.78 % Favored : 94.15 % Rotamer: Outliers : 1.86 % Allowed : 10.77 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.17), residues: 2700 helix: 1.00 (0.15), residues: 1194 sheet: 0.39 (0.28), residues: 327 loop : -0.75 (0.20), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 691 TYR 0.025 0.001 TYR C 679 PHE 0.026 0.002 PHE C 354 TRP 0.018 0.002 TRP A 917 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00269 (22011) covalent geometry : angle 0.61403 (29697) hydrogen bonds : bond 0.04169 ( 942) hydrogen bonds : angle 4.63053 ( 2589) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 257 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6857 (pp30) REVERT: A 477 MET cc_start: 0.7943 (mmm) cc_final: 0.6836 (mtt) REVERT: A 985 ARG cc_start: 0.5201 (mmt180) cc_final: 0.4236 (mtt180) REVERT: B 111 THR cc_start: 0.9187 (m) cc_final: 0.8793 (p) REVERT: B 258 CYS cc_start: 0.8519 (t) cc_final: 0.8109 (t) REVERT: B 477 MET cc_start: 0.7428 (mmm) cc_final: 0.6990 (mmp) REVERT: B 611 PHE cc_start: 0.7169 (m-80) cc_final: 0.6959 (m-80) REVERT: B 963 ASN cc_start: 0.6700 (m-40) cc_final: 0.6407 (t0) REVERT: C 477 MET cc_start: 0.7574 (mmt) cc_final: 0.6887 (mmt) REVERT: C 556 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6667 (mt-10) REVERT: C 562 TYR cc_start: 0.8488 (t80) cc_final: 0.7980 (t80) REVERT: C 595 LEU cc_start: 0.8127 (mt) cc_final: 0.7759 (mt) REVERT: C 682 LYS cc_start: 0.7457 (mttt) cc_final: 0.7176 (mmmt) REVERT: C 775 MET cc_start: 0.5083 (mtt) cc_final: 0.4571 (ttm) REVERT: C 826 GLN cc_start: 0.7070 (mp10) cc_final: 0.6748 (mp10) REVERT: C 838 LYS cc_start: 0.7508 (mmmt) cc_final: 0.7213 (ptpt) REVERT: C 881 LEU cc_start: 0.7775 (tp) cc_final: 0.6996 (pp) REVERT: C 917 TRP cc_start: 0.3624 (p90) cc_final: 0.2118 (p90) REVERT: C 963 ASN cc_start: 0.6872 (m-40) cc_final: 0.6449 (t0) outliers start: 45 outliers final: 26 residues processed: 293 average time/residue: 0.1192 time to fit residues: 56.7782 Evaluate side-chains 241 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 715 TYR Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 143 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 9 optimal weight: 0.0070 chunk 92 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 chunk 263 optimal weight: 0.0370 chunk 161 optimal weight: 0.2980 chunk 237 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN A 411 GLN ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 HIS A 865 ASN A 880 GLN B 155 ASN C 151 GLN C 657 GLN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 865 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.168978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.142784 restraints weight = 39426.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.139296 restraints weight = 59469.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.137731 restraints weight = 45086.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.137657 restraints weight = 43112.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.136992 restraints weight = 38026.346| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22011 Z= 0.110 Angle : 0.588 11.098 29697 Z= 0.304 Chirality : 0.040 0.245 3420 Planarity : 0.003 0.039 3765 Dihedral : 4.646 29.785 2872 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.63 % Favored : 94.30 % Rotamer: Outliers : 2.06 % Allowed : 11.43 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.17), residues: 2700 helix: 1.17 (0.16), residues: 1191 sheet: 0.33 (0.29), residues: 327 loop : -0.95 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 691 TYR 0.021 0.001 TYR B 594 PHE 0.021 0.001 PHE A 354 TRP 0.019 0.001 TRP A1005 HIS 0.005 0.001 HIS C 731 Details of bonding type rmsd covalent geometry : bond 0.00233 (22011) covalent geometry : angle 0.58848 (29697) hydrogen bonds : bond 0.03582 ( 942) hydrogen bonds : angle 4.42678 ( 2589) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 238 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LYS cc_start: 0.8456 (tppt) cc_final: 0.7792 (mtmm) REVERT: A 477 MET cc_start: 0.7900 (mmm) cc_final: 0.6926 (mtt) REVERT: A 985 ARG cc_start: 0.5245 (mmt180) cc_final: 0.4231 (mtt180) REVERT: B 111 THR cc_start: 0.9185 (m) cc_final: 0.8807 (p) REVERT: B 258 CYS cc_start: 0.8409 (t) cc_final: 0.8106 (t) REVERT: B 477 MET cc_start: 0.7519 (mmm) cc_final: 0.7258 (mmt) REVERT: B 963 ASN cc_start: 0.6606 (m-40) cc_final: 0.6388 (t0) REVERT: C 136 GLU cc_start: 0.6761 (tm-30) cc_final: 0.6458 (tm-30) REVERT: C 477 MET cc_start: 0.7504 (mmt) cc_final: 0.6749 (mmt) REVERT: C 506 MET cc_start: 0.7650 (mmm) cc_final: 0.7390 (tpp) REVERT: C 556 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6753 (mt-10) REVERT: C 595 LEU cc_start: 0.8147 (mt) cc_final: 0.7783 (mt) REVERT: C 775 MET cc_start: 0.5034 (mtt) cc_final: 0.4669 (ttm) REVERT: C 917 TRP cc_start: 0.3555 (p90) cc_final: 0.2177 (p90) REVERT: C 963 ASN cc_start: 0.6372 (m-40) cc_final: 0.6164 (t0) outliers start: 50 outliers final: 24 residues processed: 277 average time/residue: 0.1142 time to fit residues: 50.9835 Evaluate side-chains 232 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 957 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 207 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 218 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 32 optimal weight: 0.0010 chunk 169 optimal weight: 0.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN A 411 GLN ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.168166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.136250 restraints weight = 39514.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.133622 restraints weight = 59286.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.130118 restraints weight = 48241.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.130146 restraints weight = 49211.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.130413 restraints weight = 41795.655| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22011 Z= 0.121 Angle : 0.584 8.341 29697 Z= 0.301 Chirality : 0.040 0.202 3420 Planarity : 0.003 0.037 3765 Dihedral : 4.565 28.189 2871 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.78 % Favored : 94.15 % Rotamer: Outliers : 1.73 % Allowed : 12.50 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2700 helix: 1.24 (0.16), residues: 1191 sheet: 0.23 (0.29), residues: 309 loop : -1.08 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 691 TYR 0.012 0.001 TYR A 594 PHE 0.029 0.001 PHE B 684 TRP 0.013 0.001 TRP A1005 HIS 0.005 0.001 HIS C 731 Details of bonding type rmsd covalent geometry : bond 0.00270 (22011) covalent geometry : angle 0.58372 (29697) hydrogen bonds : bond 0.03501 ( 942) hydrogen bonds : angle 4.32989 ( 2589) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 MET cc_start: 0.7885 (mmm) cc_final: 0.7231 (mtt) REVERT: A 985 ARG cc_start: 0.5339 (mmt180) cc_final: 0.4209 (ttt180) REVERT: B 111 THR cc_start: 0.9267 (m) cc_final: 0.8913 (p) REVERT: B 477 MET cc_start: 0.7594 (mmm) cc_final: 0.7309 (mmt) REVERT: B 790 LEU cc_start: 0.7168 (tp) cc_final: 0.6966 (tp) REVERT: B 793 MET cc_start: 0.6994 (tpp) cc_final: 0.6027 (ttt) REVERT: B 963 ASN cc_start: 0.6710 (m-40) cc_final: 0.6328 (t0) REVERT: C 477 MET cc_start: 0.7550 (mmt) cc_final: 0.6787 (mmt) REVERT: C 556 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6794 (mt-10) REVERT: C 902 HIS cc_start: 0.4789 (OUTLIER) cc_final: 0.4412 (t-170) REVERT: C 912 LEU cc_start: 0.7429 (tt) cc_final: 0.6444 (mt) REVERT: C 917 TRP cc_start: 0.3171 (p90) cc_final: 0.1907 (p90) outliers start: 42 outliers final: 29 residues processed: 262 average time/residue: 0.1287 time to fit residues: 55.6365 Evaluate side-chains 236 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 957 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 902 HIS Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 247 optimal weight: 7.9990 chunk 224 optimal weight: 30.0000 chunk 138 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS A 404 HIS A 411 GLN ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 ASN B 155 ASN B 372 GLN B 417 ASN B 433 GLN ** B 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 989 GLN C 355 HIS C 433 GLN ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 865 ASN C 940 GLN C 963 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.156670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.129406 restraints weight = 39496.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124745 restraints weight = 62704.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123310 restraints weight = 61707.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.122648 restraints weight = 59642.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.122378 restraints weight = 45936.551| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.111 22011 Z= 0.491 Angle : 1.016 13.784 29697 Z= 0.516 Chirality : 0.054 0.239 3420 Planarity : 0.006 0.067 3765 Dihedral : 5.977 33.700 2871 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.07 % Favored : 91.85 % Rotamer: Outliers : 3.26 % Allowed : 12.67 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.16), residues: 2700 helix: -0.14 (0.14), residues: 1251 sheet: -0.81 (0.28), residues: 351 loop : -1.68 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 492 TYR 0.024 0.003 TYR C 493 PHE 0.045 0.004 PHE C 117 TRP 0.024 0.003 TRP C 655 HIS 0.015 0.002 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.01163 (22011) covalent geometry : angle 1.01619 (29697) hydrogen bonds : bond 0.06445 ( 942) hydrogen bonds : angle 5.47764 ( 2589) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 215 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 781 ILE cc_start: 0.6764 (OUTLIER) cc_final: 0.6489 (mt) REVERT: B 274 MET cc_start: 0.7733 (mtp) cc_final: 0.7532 (mtm) REVERT: B 477 MET cc_start: 0.7681 (mmm) cc_final: 0.7349 (mmt) REVERT: B 599 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8787 (m-10) REVERT: B 793 MET cc_start: 0.7299 (tpp) cc_final: 0.6999 (ttt) REVERT: B 958 MET cc_start: 0.7871 (tpp) cc_final: 0.7577 (tpp) REVERT: B 963 ASN cc_start: 0.6818 (m-40) cc_final: 0.6512 (t0) REVERT: C 477 MET cc_start: 0.7964 (mmt) cc_final: 0.7285 (mmt) REVERT: C 917 TRP cc_start: 0.4552 (p90) cc_final: 0.3760 (p90) outliers start: 79 outliers final: 57 residues processed: 273 average time/residue: 0.1093 time to fit residues: 49.3427 Evaluate side-chains 236 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 177 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 715 TYR Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 957 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 931 PHE Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 4 optimal weight: 0.8980 chunk 190 optimal weight: 0.5980 chunk 172 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 266 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 GLN A 601 HIS A 657 GLN A 865 ASN A 963 ASN B 155 ASN B 989 GLN C 657 GLN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 HIS C 963 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.163021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.131486 restraints weight = 38926.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127180 restraints weight = 58854.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.125642 restraints weight = 48664.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.125635 restraints weight = 48886.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.125645 restraints weight = 39793.613| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22011 Z= 0.138 Angle : 0.653 10.239 29697 Z= 0.336 Chirality : 0.042 0.172 3420 Planarity : 0.004 0.044 3765 Dihedral : 5.233 36.516 2871 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.37 % Favored : 93.56 % Rotamer: Outliers : 2.35 % Allowed : 13.74 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.17), residues: 2700 helix: 0.54 (0.15), residues: 1242 sheet: -0.39 (0.29), residues: 330 loop : -1.64 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 691 TYR 0.019 0.001 TYR C 562 PHE 0.019 0.002 PHE A 957 TRP 0.024 0.002 TRP C 917 HIS 0.019 0.001 HIS C 869 Details of bonding type rmsd covalent geometry : bond 0.00312 (22011) covalent geometry : angle 0.65265 (29697) hydrogen bonds : bond 0.03882 ( 942) hydrogen bonds : angle 4.64517 ( 2589) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 205 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 781 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6548 (mt) REVERT: B 111 THR cc_start: 0.9374 (m) cc_final: 0.9069 (p) REVERT: B 274 MET cc_start: 0.7561 (mtp) cc_final: 0.7307 (mtm) REVERT: B 477 MET cc_start: 0.7657 (mmm) cc_final: 0.7281 (mmt) REVERT: B 793 MET cc_start: 0.7395 (tpp) cc_final: 0.6982 (ttt) REVERT: B 886 LEU cc_start: 0.6990 (mm) cc_final: 0.6670 (tp) REVERT: B 963 ASN cc_start: 0.6818 (m-40) cc_final: 0.6450 (t0) REVERT: C 477 MET cc_start: 0.7911 (mmt) cc_final: 0.7124 (mmt) REVERT: C 556 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6984 (mt-10) REVERT: C 912 LEU cc_start: 0.7090 (tt) cc_final: 0.5759 (mt) REVERT: C 917 TRP cc_start: 0.4095 (p90) cc_final: 0.3709 (p90) outliers start: 57 outliers final: 37 residues processed: 244 average time/residue: 0.1316 time to fit residues: 52.6453 Evaluate side-chains 226 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 715 TYR Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 957 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 931 PHE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 266 optimal weight: 0.9990 chunk 132 optimal weight: 0.0010 chunk 33 optimal weight: 0.0470 chunk 232 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 269 optimal weight: 7.9990 chunk 214 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 127 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 GLN A 601 HIS B 357 HIS B 563 GLN B 908 GLN C 657 GLN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.165250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.131905 restraints weight = 39374.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.129465 restraints weight = 60054.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.127561 restraints weight = 45577.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126367 restraints weight = 44508.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.126995 restraints weight = 41180.439| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22011 Z= 0.112 Angle : 0.613 14.302 29697 Z= 0.311 Chirality : 0.040 0.167 3420 Planarity : 0.004 0.047 3765 Dihedral : 4.852 32.314 2871 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.56 % Favored : 93.37 % Rotamer: Outliers : 1.73 % Allowed : 14.69 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.17), residues: 2700 helix: 0.82 (0.15), residues: 1242 sheet: -0.15 (0.30), residues: 315 loop : -1.72 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 691 TYR 0.013 0.001 TYR C 679 PHE 0.038 0.001 PHE A 354 TRP 0.019 0.002 TRP C 917 HIS 0.006 0.001 HIS C 731 Details of bonding type rmsd covalent geometry : bond 0.00242 (22011) covalent geometry : angle 0.61292 (29697) hydrogen bonds : bond 0.03313 ( 942) hydrogen bonds : angle 4.41006 ( 2589) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 211 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 THR cc_start: 0.9277 (m) cc_final: 0.9058 (p) REVERT: B 274 MET cc_start: 0.7539 (mtp) cc_final: 0.7302 (mtm) REVERT: B 477 MET cc_start: 0.7676 (mmm) cc_final: 0.7254 (mmt) REVERT: B 775 MET cc_start: 0.6031 (mmm) cc_final: 0.5580 (mmm) REVERT: B 963 ASN cc_start: 0.6745 (m-40) cc_final: 0.6387 (t0) REVERT: C 477 MET cc_start: 0.7963 (mmt) cc_final: 0.7085 (mmt) REVERT: C 556 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6961 (mt-10) REVERT: C 657 GLN cc_start: 0.6130 (OUTLIER) cc_final: 0.5830 (pm20) REVERT: C 793 MET cc_start: 0.5825 (tpp) cc_final: 0.5592 (tpp) REVERT: C 912 LEU cc_start: 0.7086 (tt) cc_final: 0.5775 (mt) REVERT: C 917 TRP cc_start: 0.3732 (p90) cc_final: 0.3493 (p90) REVERT: C 998 GLN cc_start: 0.7765 (tp40) cc_final: 0.7528 (tp40) outliers start: 42 outliers final: 34 residues processed: 244 average time/residue: 0.1095 time to fit residues: 44.2392 Evaluate side-chains 226 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 957 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 657 GLN Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 825 ILE Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 931 PHE Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 7.9990 chunk 217 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 161 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 601 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.163265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.127604 restraints weight = 39359.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.126465 restraints weight = 58382.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.126482 restraints weight = 48775.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.125496 restraints weight = 36736.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.126095 restraints weight = 34184.017| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22011 Z= 0.147 Angle : 0.648 14.590 29697 Z= 0.326 Chirality : 0.041 0.177 3420 Planarity : 0.004 0.047 3765 Dihedral : 4.847 31.247 2871 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.74 % Favored : 93.19 % Rotamer: Outliers : 1.77 % Allowed : 14.93 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.17), residues: 2700 helix: 0.90 (0.15), residues: 1224 sheet: -0.22 (0.30), residues: 303 loop : -1.71 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 691 TYR 0.031 0.001 TYR B 679 PHE 0.030 0.002 PHE A 354 TRP 0.027 0.002 TRP B 954 HIS 0.007 0.001 HIS C 731 Details of bonding type rmsd covalent geometry : bond 0.00342 (22011) covalent geometry : angle 0.64799 (29697) hydrogen bonds : bond 0.03547 ( 942) hydrogen bonds : angle 4.46672 ( 2589) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 850 LEU cc_start: 0.7409 (pp) cc_final: 0.7207 (mt) REVERT: A 965 LYS cc_start: 0.6216 (mmpt) cc_final: 0.6013 (mmpt) REVERT: B 111 THR cc_start: 0.9318 (m) cc_final: 0.9083 (p) REVERT: B 274 MET cc_start: 0.7653 (mtp) cc_final: 0.7361 (mtm) REVERT: B 477 MET cc_start: 0.7641 (mmm) cc_final: 0.7186 (mmt) REVERT: B 775 MET cc_start: 0.6006 (mmm) cc_final: 0.5617 (mmm) REVERT: B 886 LEU cc_start: 0.6868 (mm) cc_final: 0.6537 (tp) REVERT: B 963 ASN cc_start: 0.6630 (m-40) cc_final: 0.6327 (t0) REVERT: C 477 MET cc_start: 0.8020 (mmt) cc_final: 0.7186 (mmt) REVERT: C 556 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6975 (mt-10) REVERT: C 912 LEU cc_start: 0.7038 (tt) cc_final: 0.5716 (mt) REVERT: C 917 TRP cc_start: 0.3909 (p90) cc_final: 0.3594 (p90) REVERT: C 1007 PHE cc_start: 0.8052 (m-10) cc_final: 0.7848 (m-10) outliers start: 43 outliers final: 37 residues processed: 235 average time/residue: 0.1218 time to fit residues: 47.9877 Evaluate side-chains 231 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 957 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 825 ILE Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 931 PHE Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 7 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 238 optimal weight: 3.9990 chunk 237 optimal weight: 0.0010 chunk 28 optimal weight: 0.0980 chunk 81 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 601 HIS A 657 GLN ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN C 657 GLN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.165531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.115649 restraints weight = 39447.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114285 restraints weight = 29729.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114615 restraints weight = 24888.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114769 restraints weight = 24584.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115189 restraints weight = 22076.747| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22011 Z= 0.114 Angle : 0.628 15.293 29697 Z= 0.314 Chirality : 0.040 0.215 3420 Planarity : 0.003 0.046 3765 Dihedral : 4.737 32.695 2871 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.52 % Favored : 93.41 % Rotamer: Outliers : 1.49 % Allowed : 15.43 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.17), residues: 2700 helix: 0.97 (0.16), residues: 1230 sheet: -0.66 (0.29), residues: 339 loop : -1.58 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 691 TYR 0.030 0.001 TYR B 679 PHE 0.038 0.001 PHE A 354 TRP 0.045 0.002 TRP C1005 HIS 0.007 0.001 HIS C 731 Details of bonding type rmsd covalent geometry : bond 0.00249 (22011) covalent geometry : angle 0.62805 (29697) hydrogen bonds : bond 0.03144 ( 942) hydrogen bonds : angle 4.34421 ( 2589) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 850 LEU cc_start: 0.7949 (pp) cc_final: 0.7354 (mt) REVERT: B 111 THR cc_start: 0.9287 (m) cc_final: 0.9050 (p) REVERT: B 477 MET cc_start: 0.7212 (mmm) cc_final: 0.6730 (mmt) REVERT: B 775 MET cc_start: 0.5488 (mmm) cc_final: 0.5108 (mmm) REVERT: C 477 MET cc_start: 0.7785 (mmt) cc_final: 0.6890 (mmt) REVERT: C 556 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6736 (mt-10) REVERT: C 562 TYR cc_start: 0.8329 (t80) cc_final: 0.7661 (t80) REVERT: C 657 GLN cc_start: 0.6634 (OUTLIER) cc_final: 0.6359 (pm20) REVERT: C 793 MET cc_start: 0.6001 (tpp) cc_final: 0.5663 (tpp) REVERT: C 912 LEU cc_start: 0.7624 (tt) cc_final: 0.5713 (mt) REVERT: C 917 TRP cc_start: 0.3371 (p90) cc_final: 0.2962 (p90) outliers start: 36 outliers final: 30 residues processed: 239 average time/residue: 0.1207 time to fit residues: 48.0842 Evaluate side-chains 226 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 957 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 657 GLN Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 825 ILE Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 931 PHE Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 127 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 201 optimal weight: 0.9980 chunk 190 optimal weight: 0.7980 chunk 159 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 417 ASN A 601 HIS A 826 GLN ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 963 ASN C 657 GLN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.163865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.131440 restraints weight = 39895.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.127515 restraints weight = 59950.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.125283 restraints weight = 47909.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.125636 restraints weight = 48021.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.125861 restraints weight = 36192.730| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22011 Z= 0.128 Angle : 0.639 15.000 29697 Z= 0.322 Chirality : 0.041 0.254 3420 Planarity : 0.004 0.046 3765 Dihedral : 4.690 30.563 2871 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.78 % Favored : 93.15 % Rotamer: Outliers : 1.65 % Allowed : 15.39 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.17), residues: 2700 helix: 0.97 (0.15), residues: 1230 sheet: -0.49 (0.29), residues: 336 loop : -1.63 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 691 TYR 0.025 0.001 TYR B 679 PHE 0.040 0.001 PHE A 354 TRP 0.037 0.002 TRP C1005 HIS 0.015 0.001 HIS B 731 Details of bonding type rmsd covalent geometry : bond 0.00293 (22011) covalent geometry : angle 0.63895 (29697) hydrogen bonds : bond 0.03281 ( 942) hydrogen bonds : angle 4.36995 ( 2589) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3197.39 seconds wall clock time: 56 minutes 14.61 seconds (3374.61 seconds total)