Starting phenix.real_space_refine on Wed May 21 17:02:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fw2_29496/05_2025/8fw2_29496_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fw2_29496/05_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_29496/05_2025/8fw2_29496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fw2_29496/05_2025/8fw2_29496.map" model { file = "/net/cci-nas-00/data/ceres_data/8fw2_29496/05_2025/8fw2_29496_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fw2_29496/05_2025/8fw2_29496_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.38, per 1000 atoms: 0.62 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: 5.29 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 3.15 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: 8.17 Time building geometry restraints manager: 6.17 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: 0.08 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: 9.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.970 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 50.330 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.100 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (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 TRP 0.034 0.005 TRP C 917 HIS 0.004 0.001 HIS C 364 PHE 0.024 0.003 PHE B 253 TYR 0.029 0.004 TYR B 449 ARG 0.003 0.000 ARG A 285 Details of bonding type rmsd hydrogen bonds : bond 0.18966 ( 942) hydrogen bonds : angle 6.75040 ( 2589) covalent geometry : bond 0.01127 (22011) covalent geometry : angle 1.16074 (29697) *********************** 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 : 2.158 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: 0.6655 (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: 0.7495 (mmt) REVERT: C 547 LYS cc_start: 0.7234 (mttt) cc_final: 0.7010 (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: 0.5758 (m-10) REVERT: C 875 MET cc_start: 0.5206 (mtt) cc_final: 0.4066 (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: 0.3639 time to fit residues: 321.4564 Evaluate side-chains 278 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 3.843 ------------------------------------------------------------------------------- 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 227 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 245 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 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 B 989 GLN C 147 HIS C 269 HIS C 273 ASN C 348 GLN C 411 GLN C 587 ASN ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 797 HIS C 940 GLN C 943 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.169129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.133570 restraints weight = 39325.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.129320 restraints weight = 56747.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.129383 restraints weight = 41921.125| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22011 Z= 0.167 Angle : 0.709 11.931 29697 Z= 0.372 Chirality : 0.043 0.173 3420 Planarity : 0.004 0.055 3765 Dihedral : 4.994 31.200 2873 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.04 % Favored : 94.81 % Rotamer: Outliers : 2.06 % Allowed : 8.50 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2700 helix: 0.81 (0.15), residues: 1176 sheet: 0.56 (0.28), residues: 327 loop : -0.77 (0.19), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 917 HIS 0.007 0.001 HIS C 797 PHE 0.028 0.002 PHE A 969 TYR 0.017 0.002 TYR A 594 ARG 0.008 0.001 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.04878 ( 942) hydrogen bonds : angle 4.92811 ( 2589) covalent geometry : bond 0.00367 (22011) covalent geometry : angle 0.70917 (29697) *********************** 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 386 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 336 time to evaluate : 2.386 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: 0.7563 (t80) cc_final: 0.7344 (t80) REVERT: A 586 ILE cc_start: 0.8130 (mm) cc_final: 0.7650 (mm) REVERT: A 985 ARG cc_start: 0.5194 (mmt180) cc_final: 0.4320 (mtt180) REVERT: B 111 THR cc_start: 0.9236 (m) cc_final: 0.8819 (p) REVERT: B 256 GLN cc_start: 0.7921 (pm20) cc_final: 0.7662 (pp30) REVERT: B 258 CYS cc_start: 0.8425 (t) cc_final: 0.8137 (t) REVERT: B 274 MET cc_start: 0.7343 (mtp) cc_final: 0.7075 (mtt) REVERT: B 963 ASN cc_start: 0.6776 (m-40) cc_final: 0.6350 (t0) REVERT: B 985 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7918 (mmm-85) REVERT: C 238 LYS cc_start: 0.8989 (tmtt) cc_final: 0.8716 (tmmt) REVERT: C 477 MET cc_start: 0.7593 (mmt) cc_final: 0.6884 (mmt) REVERT: C 562 TYR cc_start: 0.8465 (t80) cc_final: 0.7948 (t80) REVERT: C 574 GLU cc_start: 0.7752 (tp30) cc_final: 0.7520 (tp30) REVERT: C 838 LYS cc_start: 0.7566 (mmmt) cc_final: 0.7124 (ptpt) REVERT: C 902 HIS cc_start: 0.5503 (OUTLIER) cc_final: 0.4717 (t-170) REVERT: C 917 TRP cc_start: 0.3778 (p90) cc_final: 0.2224 (p90) REVERT: C 963 ASN cc_start: 0.7522 (m-40) cc_final: 0.6859 (t0) outliers start: 50 outliers final: 32 residues processed: 373 average time/residue: 0.3268 time to fit residues: 190.0172 Evaluate side-chains 246 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 2.456 ------------------------------------------------------------------------------- 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 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 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 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 160 optimal weight: 0.9990 chunk 233 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 258 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 94 optimal weight: 0.1980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 ASN B 146 HIS B 155 ASN B 744 HIS B 943 ASN C 657 GLN ** 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 = 0.4193 r_free = 0.4193 target = 0.166852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.134533 restraints weight = 39008.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.129530 restraints weight = 58625.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.128386 restraints weight = 45924.631| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22011 Z= 0.150 Angle : 0.631 11.411 29697 Z= 0.330 Chirality : 0.041 0.229 3420 Planarity : 0.004 0.048 3765 Dihedral : 4.851 29.816 2873 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.89 % Favored : 94.04 % Rotamer: Outliers : 1.90 % Allowed : 10.85 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2700 helix: 0.97 (0.15), residues: 1197 sheet: 0.39 (0.29), residues: 315 loop : -0.87 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 917 HIS 0.014 0.001 HIS A 269 PHE 0.023 0.002 PHE C 354 TYR 0.031 0.002 TYR C 679 ARG 0.007 0.000 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 942) hydrogen bonds : angle 4.66655 ( 2589) covalent geometry : bond 0.00334 (22011) covalent geometry : angle 0.63112 (29697) *********************** 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 287 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 MET cc_start: 0.7824 (mmm) cc_final: 0.6954 (mtt) REVERT: A 823 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7206 (pt0) REVERT: A 824 GLU cc_start: 0.7905 (mp0) cc_final: 0.7659 (mp0) REVERT: A 985 ARG cc_start: 0.5138 (mmt180) cc_final: 0.4238 (mtt180) REVERT: B 111 THR cc_start: 0.9241 (m) cc_final: 0.8882 (p) REVERT: B 258 CYS cc_start: 0.8522 (t) cc_final: 0.8221 (t) REVERT: B 477 MET cc_start: 0.7459 (mmm) cc_final: 0.7022 (mmp) REVERT: B 594 TYR cc_start: 0.7633 (p90) cc_final: 0.6931 (p90) REVERT: B 768 LEU cc_start: 0.7950 (tp) cc_final: 0.7636 (tt) REVERT: B 963 ASN cc_start: 0.6699 (m-40) cc_final: 0.6417 (t0) REVERT: C 477 MET cc_start: 0.7621 (mmt) cc_final: 0.6947 (mmt) REVERT: C 556 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6775 (mt-10) REVERT: C 562 TYR cc_start: 0.8454 (t80) cc_final: 0.7930 (t80) REVERT: C 595 LEU cc_start: 0.8199 (mt) cc_final: 0.7857 (mt) REVERT: C 682 LYS cc_start: 0.7456 (mttt) cc_final: 0.7190 (mmmt) REVERT: C 775 MET cc_start: 0.5124 (mtt) cc_final: 0.4605 (ttm) REVERT: C 838 LYS cc_start: 0.7453 (mmmt) cc_final: 0.7182 (ptpt) REVERT: C 881 LEU cc_start: 0.7781 (tp) cc_final: 0.7161 (pp) REVERT: C 885 MET cc_start: 0.7816 (mmm) cc_final: 0.7571 (mtt) REVERT: C 917 TRP cc_start: 0.3702 (p90) cc_final: 0.2348 (p90) REVERT: C 963 ASN cc_start: 0.6851 (m-40) cc_final: 0.6420 (t0) outliers start: 46 outliers final: 30 residues processed: 277 average time/residue: 0.3022 time to fit residues: 135.3970 Evaluate side-chains 236 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 361 THR 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 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 A residue 823 GLU 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 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 218 ASP Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 480 ILE 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 677 ILE Chi-restraints excluded: chain C residue 769 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 62 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 185 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS A 268 ASN A 404 HIS ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 HIS B 433 GLN ** B 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.159168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.131621 restraints weight = 39199.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.127273 restraints weight = 60628.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.125396 restraints weight = 52711.943| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 22011 Z= 0.344 Angle : 0.844 10.358 29697 Z= 0.434 Chirality : 0.049 0.219 3420 Planarity : 0.005 0.058 3765 Dihedral : 5.678 35.019 2872 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.96 % Favored : 92.93 % Rotamer: Outliers : 3.34 % Allowed : 11.59 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), residues: 2700 helix: 0.20 (0.15), residues: 1245 sheet: -0.12 (0.29), residues: 321 loop : -1.42 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A1005 HIS 0.012 0.002 HIS C 110 PHE 0.034 0.003 PHE C 201 TYR 0.020 0.003 TYR C 679 ARG 0.006 0.001 ARG B 691 Details of bonding type rmsd hydrogen bonds : bond 0.05646 ( 942) hydrogen bonds : angle 5.16299 ( 2589) covalent geometry : bond 0.00799 (22011) covalent geometry : angle 0.84437 (29697) *********************** 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 299 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 218 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 823 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7131 (pt0) REVERT: B 111 THR cc_start: 0.9436 (m) cc_final: 0.9091 (p) REVERT: B 477 MET cc_start: 0.7762 (mmm) cc_final: 0.7460 (mmt) REVERT: B 594 TYR cc_start: 0.7705 (p90) cc_final: 0.7093 (p90) REVERT: B 963 ASN cc_start: 0.6855 (m-40) cc_final: 0.6541 (t0) REVERT: C 349 MET cc_start: 0.8122 (mtp) cc_final: 0.7865 (mtm) REVERT: C 477 MET cc_start: 0.7984 (mmt) cc_final: 0.7312 (mmt) REVERT: C 556 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7041 (mt-10) REVERT: C 917 TRP cc_start: 0.4442 (p90) cc_final: 0.4081 (p90) REVERT: C 963 ASN cc_start: 0.6803 (m-40) cc_final: 0.6411 (t0) outliers start: 81 outliers final: 57 residues processed: 281 average time/residue: 0.2970 time to fit residues: 134.8125 Evaluate side-chains 246 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 134 PHE 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 322 LEU 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 658 GLU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 693 GLN 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 823 GLU Chi-restraints excluded: chain A residue 846 ASN 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 220 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 672 LEU 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 957 PHE Chi-restraints excluded: chain B residue 987 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 313 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 495 CYS Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 825 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 26 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 195 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 179 optimal weight: 8.9990 chunk 168 optimal weight: 20.0000 chunk 219 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN A 411 GLN A 601 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 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 940 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.163564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.136279 restraints weight = 37984.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131765 restraints weight = 53267.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.129573 restraints weight = 52347.296| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22011 Z= 0.128 Angle : 0.601 8.313 29697 Z= 0.314 Chirality : 0.041 0.158 3420 Planarity : 0.004 0.050 3765 Dihedral : 5.088 36.100 2872 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.15 % Favored : 93.78 % Rotamer: Outliers : 2.76 % Allowed : 12.42 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2700 helix: 0.75 (0.15), residues: 1230 sheet: -0.53 (0.28), residues: 351 loop : -1.29 (0.20), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 917 HIS 0.004 0.001 HIS B 797 PHE 0.024 0.001 PHE B 684 TYR 0.018 0.001 TYR C 562 ARG 0.007 0.000 ARG C 492 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 942) hydrogen bonds : angle 4.55851 ( 2589) covalent geometry : bond 0.00282 (22011) covalent geometry : angle 0.60085 (29697) *********************** 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 284 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 217 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7334 (pp30) REVERT: A 739 LYS cc_start: 0.7445 (mtpt) cc_final: 0.7155 (mttp) REVERT: A 824 GLU cc_start: 0.8176 (mp0) cc_final: 0.7844 (mp0) REVERT: B 111 THR cc_start: 0.9354 (m) cc_final: 0.9059 (p) REVERT: B 477 MET cc_start: 0.7715 (mmm) cc_final: 0.7377 (mmt) REVERT: B 793 MET cc_start: 0.7132 (tpp) cc_final: 0.6890 (ttt) REVERT: B 886 LEU cc_start: 0.6934 (mm) cc_final: 0.6724 (tp) REVERT: B 963 ASN cc_start: 0.6656 (m-40) cc_final: 0.6344 (t0) REVERT: C 477 MET cc_start: 0.8041 (mmt) cc_final: 0.7238 (mmt) REVERT: C 556 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6945 (mt-10) REVERT: C 562 TYR cc_start: 0.8423 (t80) cc_final: 0.7798 (t80) REVERT: C 691 ARG cc_start: 0.7562 (mtt90) cc_final: 0.7332 (mtt90) REVERT: C 775 MET cc_start: 0.5534 (mtt) cc_final: 0.4433 (tmm) REVERT: C 793 MET cc_start: 0.6267 (tpp) cc_final: 0.6058 (tpp) REVERT: C 963 ASN cc_start: 0.6575 (m-40) cc_final: 0.6315 (t0) outliers start: 67 outliers final: 41 residues processed: 268 average time/residue: 0.2967 time to fit residues: 127.4728 Evaluate side-chains 235 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 2.433 ------------------------------------------------------------------------------- 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 241 GLN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU 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 541 THR 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 950 SER Chi-restraints excluded: chain A residue 952 ASP 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 220 LEU Chi-restraints excluded: chain B residue 387 ILE 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 746 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 218 ASP Chi-restraints excluded: chain C residue 274 MET 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 835 ASN Chi-restraints excluded: chain C residue 838 LYS Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 927 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 265 optimal weight: 6.9990 chunk 246 optimal weight: 8.9990 chunk 249 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 GLN B 989 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.159741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.130315 restraints weight = 37895.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.126349 restraints weight = 59804.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.124120 restraints weight = 54623.912| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 22011 Z= 0.263 Angle : 0.723 9.515 29697 Z= 0.372 Chirality : 0.044 0.178 3420 Planarity : 0.004 0.050 3765 Dihedral : 5.318 33.105 2872 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer: Outliers : 2.93 % Allowed : 13.78 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.17), residues: 2700 helix: 0.56 (0.15), residues: 1230 sheet: -0.18 (0.30), residues: 303 loop : -1.61 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 917 HIS 0.008 0.001 HIS C 110 PHE 0.032 0.002 PHE B 684 TYR 0.018 0.002 TYR B 594 ARG 0.007 0.001 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 942) hydrogen bonds : angle 4.81800 ( 2589) covalent geometry : bond 0.00625 (22011) covalent geometry : angle 0.72308 (29697) *********************** 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 276 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 205 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7394 (pp30) REVERT: A 391 ASP cc_start: 0.7957 (m-30) cc_final: 0.7742 (t0) REVERT: A 850 LEU cc_start: 0.7381 (pp) cc_final: 0.7029 (mt) REVERT: B 477 MET cc_start: 0.7664 (mmm) cc_final: 0.7303 (mmt) REVERT: B 770 MET cc_start: 0.7874 (mpp) cc_final: 0.7610 (mpp) REVERT: B 793 MET cc_start: 0.7417 (tpp) cc_final: 0.7200 (ttt) REVERT: B 963 ASN cc_start: 0.6663 (m-40) cc_final: 0.6344 (t0) REVERT: C 339 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8344 (tt) REVERT: C 349 MET cc_start: 0.8086 (mtp) cc_final: 0.7808 (mtm) REVERT: C 477 MET cc_start: 0.8077 (mmt) cc_final: 0.7272 (mmt) REVERT: C 556 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7054 (mt-10) REVERT: C 684 PHE cc_start: 0.6811 (m-10) cc_final: 0.6397 (m-80) REVERT: C 963 ASN cc_start: 0.6553 (m-40) cc_final: 0.6318 (t0) REVERT: C 1005 TRP cc_start: 0.8003 (m-10) cc_final: 0.7764 (m-10) outliers start: 71 outliers final: 51 residues processed: 258 average time/residue: 0.2904 time to fit residues: 121.1676 Evaluate side-chains 247 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU 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 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 950 SER 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 220 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 715 TYR Chi-restraints excluded: chain B residue 746 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 313 LEU 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 412 ASP Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 902 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 154 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 212 optimal weight: 0.5980 chunk 158 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 ASN B 563 GLN 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 940 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.163559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.134236 restraints weight = 37802.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.130410 restraints weight = 57350.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.128707 restraints weight = 47118.516| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.5612 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= 0.120 Angle : 0.601 9.291 29697 Z= 0.310 Chirality : 0.040 0.176 3420 Planarity : 0.004 0.044 3765 Dihedral : 4.975 34.725 2872 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.26 % Favored : 93.67 % Rotamer: Outliers : 2.64 % Allowed : 14.52 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2700 helix: 0.89 (0.16), residues: 1230 sheet: -0.22 (0.30), residues: 303 loop : -1.58 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 917 HIS 0.006 0.001 HIS C 731 PHE 0.045 0.001 PHE B 684 TYR 0.013 0.001 TYR A 594 ARG 0.005 0.000 ARG C 925 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 942) hydrogen bonds : angle 4.43428 ( 2589) covalent geometry : bond 0.00262 (22011) covalent geometry : angle 0.60094 (29697) *********************** 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 286 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7431 (pp30) REVERT: A 850 LEU cc_start: 0.7317 (pp) cc_final: 0.6973 (mt) REVERT: A 965 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.4955 (mmpt) REVERT: B 111 THR cc_start: 0.9337 (m) cc_final: 0.9080 (p) REVERT: B 477 MET cc_start: 0.7669 (mmm) cc_final: 0.7300 (mmt) REVERT: B 793 MET cc_start: 0.7337 (tpp) cc_final: 0.7079 (ttt) REVERT: B 963 ASN cc_start: 0.6580 (m-40) cc_final: 0.6272 (t0) REVERT: C 477 MET cc_start: 0.8018 (mmt) cc_final: 0.7169 (mmt) REVERT: C 556 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6954 (mt-10) REVERT: C 684 PHE cc_start: 0.6770 (m-10) cc_final: 0.6328 (m-80) REVERT: C 775 MET cc_start: 0.5822 (mtt) cc_final: 0.4550 (tmm) outliers start: 64 outliers final: 46 residues processed: 267 average time/residue: 0.2906 time to fit residues: 127.0337 Evaluate side-chains 245 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU 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 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 A residue 963 ASN Chi-restraints excluded: chain A residue 965 LYS 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 339 LEU Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 646 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 715 TYR Chi-restraints excluded: chain B residue 746 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 146 HIS 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 769 ILE Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 848 VAL 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 940 GLN 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 222 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 199 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 232 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 ASN B 989 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 869 HIS C 940 GLN C 963 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.161481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.133565 restraints weight = 38629.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129227 restraints weight = 59884.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.128087 restraints weight = 50724.785| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22011 Z= 0.197 Angle : 0.677 12.394 29697 Z= 0.345 Chirality : 0.042 0.256 3420 Planarity : 0.004 0.046 3765 Dihedral : 5.085 31.655 2872 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.41 % Favored : 92.56 % Rotamer: Outliers : 2.60 % Allowed : 15.47 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2700 helix: 0.80 (0.15), residues: 1236 sheet: -0.32 (0.30), residues: 303 loop : -1.70 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 917 HIS 0.023 0.001 HIS C 869 PHE 0.045 0.002 PHE B 684 TYR 0.019 0.002 TYR B 594 ARG 0.005 0.000 ARG C 925 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 942) hydrogen bonds : angle 4.58081 ( 2589) covalent geometry : bond 0.00465 (22011) covalent geometry : angle 0.67654 (29697) *********************** 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 264 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 201 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7412 (pp30) REVERT: B 477 MET cc_start: 0.7682 (mmm) cc_final: 0.7282 (mmt) REVERT: B 793 MET cc_start: 0.7404 (tpp) cc_final: 0.7144 (ttt) REVERT: C 339 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8416 (tt) REVERT: C 477 MET cc_start: 0.8067 (mmt) cc_final: 0.7188 (mmt) REVERT: C 556 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7046 (mt-10) outliers start: 63 outliers final: 49 residues processed: 248 average time/residue: 0.2846 time to fit residues: 115.6188 Evaluate side-chains 244 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU 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 774 LYS 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 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 339 LEU Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 646 SER Chi-restraints excluded: chain B residue 715 TYR Chi-restraints excluded: chain B residue 746 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 C residue 146 HIS 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 495 CYS 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 828 VAL Chi-restraints excluded: chain C residue 848 VAL 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 940 GLN Chi-restraints excluded: chain C residue 963 ASN Chi-restraints excluded: chain C residue 1012 LEU 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 60 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 204 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 266 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 223 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS B 963 ASN B 989 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 940 GLN C 963 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.162220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.138156 restraints weight = 38645.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.134424 restraints weight = 55334.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.132729 restraints weight = 51884.279| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.5940 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 : 0.641 11.744 29697 Z= 0.327 Chirality : 0.041 0.184 3420 Planarity : 0.004 0.045 3765 Dihedral : 5.019 33.855 2872 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.89 % Favored : 93.07 % Rotamer: Outliers : 2.23 % Allowed : 15.97 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2700 helix: 0.88 (0.15), residues: 1236 sheet: -0.66 (0.29), residues: 333 loop : -1.57 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 917 HIS 0.008 0.001 HIS C 731 PHE 0.058 0.002 PHE B 684 TYR 0.016 0.001 TYR A 810 ARG 0.005 0.000 ARG C 925 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 942) hydrogen bonds : angle 4.47629 ( 2589) covalent geometry : bond 0.00340 (22011) covalent geometry : angle 0.64062 (29697) *********************** 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 252 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 198 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.8684 (mmm) cc_final: 0.8477 (mmp) REVERT: A 241 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7368 (pp30) REVERT: A 850 LEU cc_start: 0.7036 (pp) cc_final: 0.6645 (mt) REVERT: B 477 MET cc_start: 0.7698 (mmm) cc_final: 0.7277 (mmt) REVERT: C 477 MET cc_start: 0.8061 (mmt) cc_final: 0.7164 (mmt) REVERT: C 556 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6973 (mt-10) outliers start: 54 outliers final: 43 residues processed: 243 average time/residue: 0.3053 time to fit residues: 121.7865 Evaluate side-chains 232 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU 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 952 ASP Chi-restraints excluded: chain A residue 957 PHE 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 599 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 646 SER Chi-restraints excluded: chain B residue 715 TYR Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 957 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 165 CYS 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 677 ILE Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 848 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 176 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 242 optimal weight: 7.9990 chunk 256 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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** ** B 916 ASN ** 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 = 0.4123 r_free = 0.4123 target = 0.160517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.127283 restraints weight = 37996.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.124963 restraints weight = 62186.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.125760 restraints weight = 57845.216| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22011 Z= 0.202 Angle : 0.703 14.507 29697 Z= 0.357 Chirality : 0.043 0.186 3420 Planarity : 0.004 0.045 3765 Dihedral : 5.161 31.524 2872 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.33 % Favored : 91.59 % Rotamer: Outliers : 2.43 % Allowed : 15.92 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2700 helix: 0.77 (0.15), residues: 1236 sheet: -0.70 (0.29), residues: 333 loop : -1.71 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP C 917 HIS 0.007 0.001 HIS C 731 PHE 0.060 0.002 PHE B 684 TYR 0.034 0.002 TYR B 679 ARG 0.005 0.000 ARG C 270 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 942) hydrogen bonds : angle 4.65104 ( 2589) covalent geometry : bond 0.00480 (22011) covalent geometry : angle 0.70343 (29697) ********************** 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 256 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 197 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7216 (pp30) REVERT: A 391 ASP cc_start: 0.7965 (m-30) cc_final: 0.7746 (t0) REVERT: A 965 LYS cc_start: 0.6096 (mmpt) cc_final: 0.5861 (mmpt) REVERT: B 477 MET cc_start: 0.7678 (mmm) cc_final: 0.7256 (mmt) REVERT: B 868 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6235 (tp) REVERT: C 339 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8399 (tt) REVERT: C 477 MET cc_start: 0.8083 (mmt) cc_final: 0.7163 (mmt) REVERT: C 556 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7038 (mt-10) REVERT: C 594 TYR cc_start: 0.8256 (p90) cc_final: 0.7949 (p90) REVERT: C 595 LEU cc_start: 0.8517 (mt) cc_final: 0.8301 (mt) outliers start: 59 outliers final: 46 residues processed: 243 average time/residue: 0.2827 time to fit residues: 112.6913 Evaluate side-chains 238 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU 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 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 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 646 SER Chi-restraints excluded: chain B residue 715 TYR Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 868 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 146 HIS Chi-restraints excluded: chain C residue 165 CYS 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 495 CYS 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 848 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 49 optimal weight: 0.8980 chunk 127 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 236 optimal weight: 0.5980 chunk 139 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 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 601 HIS ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.160938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.135870 restraints weight = 38806.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132392 restraints weight = 59187.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.131092 restraints weight = 46642.844| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.259 22011 Z= 0.227 Angle : 0.854 59.173 29697 Z= 0.457 Chirality : 0.045 0.734 3420 Planarity : 0.004 0.047 3765 Dihedral : 5.159 31.782 2872 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.19 % Favored : 91.74 % Rotamer: Outliers : 2.31 % Allowed : 16.25 % Favored : 81.44 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2700 helix: 0.78 (0.15), residues: 1236 sheet: -0.70 (0.29), residues: 333 loop : -1.72 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 917 HIS 0.006 0.001 HIS A 508 PHE 0.048 0.002 PHE B 684 TYR 0.034 0.002 TYR B 679 ARG 0.004 0.000 ARG C 925 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 942) hydrogen bonds : angle 4.64474 ( 2589) covalent geometry : bond 0.00567 (22011) covalent geometry : angle 0.85438 (29697) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6321.56 seconds wall clock time: 112 minutes 17.59 seconds (6737.59 seconds total)