Starting phenix.real_space_refine on Wed Jun 18 21:26:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fw2_29496/06_2025/8fw2_29496_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fw2_29496/06_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_29496/06_2025/8fw2_29496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fw2_29496/06_2025/8fw2_29496.map" model { file = "/net/cci-nas-00/data/ceres_data/8fw2_29496/06_2025/8fw2_29496_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fw2_29496/06_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 15.76, per 1000 atoms: 0.73 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: 6.27 Conformation dependent library (CDL) restraints added in 2.7 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: 3.01 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: 8.91 Time building geometry restraints manager: 7.05 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: 0.07 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: 47.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 56.610 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.500 ------------------------------------------------------------------------------- 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 : 2.473 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: 0.3985 time to fit residues: 353.1872 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 : 3.530 ------------------------------------------------------------------------------- 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 = 39325.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.129308 restraints weight = 56746.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.129372 restraints weight = 41940.156| |-----------------------------------------------------------------------------| 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 : 2.742 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: 0.7345 (t80) REVERT: A 586 ILE cc_start: 0.8131 (mm) cc_final: 0.7651 (mm) REVERT: A 985 ARG cc_start: 0.5198 (mmt180) cc_final: 0.4321 (mtt180) REVERT: B 111 THR cc_start: 0.9236 (m) cc_final: 0.8818 (p) REVERT: B 256 GLN cc_start: 0.7922 (pm20) cc_final: 0.7663 (pp30) REVERT: B 258 CYS cc_start: 0.8426 (t) cc_final: 0.8138 (t) REVERT: B 274 MET cc_start: 0.7351 (mtp) cc_final: 0.7083 (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: 0.8990 (tmtt) cc_final: 0.8716 (tmmt) REVERT: C 477 MET cc_start: 0.7596 (mmt) cc_final: 0.6886 (mmt) REVERT: C 562 TYR cc_start: 0.8463 (t80) cc_final: 0.7947 (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: 0.7123 (ptpt) REVERT: C 902 HIS cc_start: 0.5503 (OUTLIER) cc_final: 0.4716 (t-170) REVERT: C 917 TRP cc_start: 0.3778 (p90) cc_final: 0.2226 (p90) REVERT: C 963 ASN cc_start: 0.7522 (m-40) cc_final: 0.6860 (t0) outliers start: 50 outliers final: 32 residues processed: 373 average time/residue: 0.3648 time to fit residues: 215.2326 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 : 2.491 ------------------------------------------------------------------------------- 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: 0.6980 chunk 130 optimal weight: 0.0670 chunk 200 optimal weight: 3.9990 chunk 258 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 94 optimal weight: 0.1980 overall best weight: 0.5520 ------------------------------------------------------------------------------- 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 269 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 ASN B 146 HIS B 155 ASN B 744 HIS B 943 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 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.168700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.134519 restraints weight = 39017.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.130703 restraints weight = 55569.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.128041 restraints weight = 43257.204| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22011 Z= 0.123 Angle : 0.612 10.807 29697 Z= 0.320 Chirality : 0.040 0.237 3420 Planarity : 0.004 0.047 3765 Dihedral : 4.773 30.144 2873 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.81 % Favored : 94.15 % Rotamer: Outliers : 1.77 % Allowed : 10.68 % Favored : 87.54 % 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: 0.27 (0.17), residues: 2700 helix: 1.10 (0.16), residues: 1176 sheet: 0.26 (0.28), residues: 345 loop : -0.74 (0.20), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 917 HIS 0.013 0.001 HIS A 269 PHE 0.026 0.002 PHE C 354 TYR 0.031 0.002 TYR C 679 ARG 0.008 0.000 ARG B 691 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 942) hydrogen bonds : angle 4.61891 ( 2589) covalent geometry : bond 0.00262 (22011) covalent geometry : angle 0.61208 (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 290 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 MET cc_start: 0.7872 (mmm) cc_final: 0.6824 (mtt) REVERT: A 798 LEU cc_start: 0.7145 (tp) cc_final: 0.6898 (tp) REVERT: A 985 ARG cc_start: 0.5194 (mmt180) cc_final: 0.4232 (mtt180) REVERT: B 111 THR cc_start: 0.9035 (m) cc_final: 0.8617 (p) REVERT: B 258 CYS cc_start: 0.8430 (t) cc_final: 0.8139 (t) REVERT: B 477 MET cc_start: 0.7375 (mmm) cc_final: 0.6957 (mmp) REVERT: B 594 TYR cc_start: 0.7742 (p90) cc_final: 0.7043 (p90) REVERT: B 768 LEU cc_start: 0.7875 (tp) cc_final: 0.7589 (tt) REVERT: B 958 MET cc_start: 0.7698 (mmp) cc_final: 0.7399 (mmm) REVERT: B 963 ASN cc_start: 0.6784 (m-40) cc_final: 0.6442 (t0) REVERT: C 274 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.7092 (mtp) REVERT: C 477 MET cc_start: 0.7569 (mmt) cc_final: 0.6864 (mmt) REVERT: C 556 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6656 (mt-10) REVERT: C 562 TYR cc_start: 0.8508 (t80) cc_final: 0.8032 (t80) REVERT: C 595 LEU cc_start: 0.8142 (mt) cc_final: 0.7803 (mt) REVERT: C 682 LYS cc_start: 0.7395 (mttt) cc_final: 0.7075 (mmmt) REVERT: C 775 MET cc_start: 0.5228 (mtt) cc_final: 0.4602 (ttm) REVERT: C 826 GLN cc_start: 0.7356 (mp10) cc_final: 0.6773 (mp10) REVERT: C 838 LYS cc_start: 0.7749 (mmmt) cc_final: 0.7287 (ptpt) REVERT: C 881 LEU cc_start: 0.7859 (tp) cc_final: 0.7132 (pp) REVERT: C 885 MET cc_start: 0.7718 (mmm) cc_final: 0.7469 (mtt) REVERT: C 917 TRP cc_start: 0.3566 (p90) cc_final: 0.2031 (p90) REVERT: C 943 ASN cc_start: 0.6285 (OUTLIER) cc_final: 0.5681 (m-40) REVERT: C 963 ASN cc_start: 0.6988 (m-40) cc_final: 0.6538 (t0) REVERT: C 983 LEU cc_start: 0.8208 (mm) cc_final: 0.7929 (tp) outliers start: 43 outliers final: 25 residues processed: 281 average time/residue: 0.3404 time to fit residues: 155.0264 Evaluate side-chains 238 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 2.896 ------------------------------------------------------------------------------- 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 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 662 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 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 274 MET 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 943 ASN 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: 8.9990 chunk 58 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 185 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS A 268 ASN A 269 HIS A 404 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN B 357 HIS ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 989 GLN C 355 HIS C 433 GLN ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.161138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.133625 restraints weight = 39633.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.129193 restraints weight = 62110.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127664 restraints weight = 56223.019| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 22011 Z= 0.299 Angle : 0.791 11.070 29697 Z= 0.407 Chirality : 0.047 0.193 3420 Planarity : 0.005 0.052 3765 Dihedral : 5.418 32.078 2872 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.44 % Favored : 93.44 % Rotamer: Outliers : 2.85 % Allowed : 11.39 % Favored : 85.77 % 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: -0.56 (0.16), residues: 2700 helix: 0.38 (0.15), residues: 1245 sheet: 0.57 (0.30), residues: 273 loop : -1.40 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1005 HIS 0.010 0.001 HIS C 110 PHE 0.034 0.003 PHE C 201 TYR 0.021 0.002 TYR C 679 ARG 0.006 0.001 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.05305 ( 942) hydrogen bonds : angle 4.99626 ( 2589) covalent geometry : bond 0.00695 (22011) covalent geometry : angle 0.79144 (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 291 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 222 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 850 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6517 (mm) REVERT: A 985 ARG cc_start: 0.5595 (mmt180) cc_final: 0.4096 (ttp-170) REVERT: B 111 THR cc_start: 0.9416 (m) cc_final: 0.9103 (p) REVERT: B 274 MET cc_start: 0.7851 (mtp) cc_final: 0.7623 (mtm) REVERT: B 477 MET cc_start: 0.7664 (mmm) cc_final: 0.7362 (mmt) REVERT: B 963 ASN cc_start: 0.6756 (m-40) cc_final: 0.6508 (t0) REVERT: C 477 MET cc_start: 0.7889 (mmt) cc_final: 0.7242 (mmt) REVERT: C 556 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7018 (mt-10) REVERT: C 881 LEU cc_start: 0.7710 (tp) cc_final: 0.7207 (pp) REVERT: C 917 TRP cc_start: 0.4639 (p90) cc_final: 0.3023 (p90) REVERT: C 963 ASN cc_start: 0.6728 (m-40) cc_final: 0.6373 (t0) outliers start: 69 outliers final: 45 residues processed: 275 average time/residue: 0.3209 time to fit residues: 144.0951 Evaluate side-chains 243 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 2.623 ------------------------------------------------------------------------------- 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 170 GLU Chi-restraints excluded: chain A residue 171 SER 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 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 735 VAL Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 850 LEU 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 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 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 662 LEU Chi-restraints excluded: chain C residue 769 ILE 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: 0.4980 chunk 201 optimal weight: 0.8980 chunk 249 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 219 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS 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 433 GLN B 989 GLN C 657 GLN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.164288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.131096 restraints weight = 38988.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.125780 restraints weight = 60957.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124596 restraints weight = 49015.109| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22011 Z= 0.127 Angle : 0.601 8.300 29697 Z= 0.312 Chirality : 0.040 0.174 3420 Planarity : 0.004 0.046 3765 Dihedral : 4.979 35.154 2872 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.19 % Favored : 93.74 % Rotamer: Outliers : 2.43 % Allowed : 12.38 % Favored : 85.19 % 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: -0.29 (0.17), residues: 2700 helix: 0.78 (0.15), residues: 1230 sheet: 0.19 (0.30), residues: 303 loop : -1.36 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 917 HIS 0.017 0.001 HIS A 269 PHE 0.024 0.001 PHE B 684 TYR 0.019 0.001 TYR B 594 ARG 0.006 0.000 ARG B 388 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 942) hydrogen bonds : angle 4.53101 ( 2589) covalent geometry : bond 0.00280 (22011) covalent geometry : angle 0.60051 (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 276 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 217 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 THR cc_start: 0.9366 (m) cc_final: 0.9046 (p) REVERT: B 274 MET cc_start: 0.7702 (mtp) cc_final: 0.7474 (mtm) REVERT: B 477 MET cc_start: 0.7590 (mmm) cc_final: 0.7270 (mmt) REVERT: B 506 MET cc_start: 0.8778 (mmm) cc_final: 0.8567 (mmm) REVERT: B 963 ASN cc_start: 0.6793 (m-40) cc_final: 0.6494 (t0) REVERT: C 477 MET cc_start: 0.7915 (mmt) cc_final: 0.7143 (mmt) REVERT: C 556 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6956 (mt-10) REVERT: C 562 TYR cc_start: 0.8387 (t80) cc_final: 0.7801 (t80) REVERT: C 691 ARG cc_start: 0.7594 (mtt90) cc_final: 0.7346 (mtt90) REVERT: C 793 MET cc_start: 0.6326 (tpp) cc_final: 0.6103 (tpp) REVERT: C 912 LEU cc_start: 0.7675 (tt) cc_final: 0.6458 (mt) REVERT: C 917 TRP cc_start: 0.4027 (p90) cc_final: 0.2482 (p90) REVERT: C 963 ASN cc_start: 0.6817 (m-40) cc_final: 0.6514 (t0) outliers start: 59 outliers final: 43 residues processed: 262 average time/residue: 0.3022 time to fit residues: 128.4026 Evaluate side-chains 233 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 2.510 ------------------------------------------------------------------------------- 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 217 CYS 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 512 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 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 221 LEU Chi-restraints excluded: chain B residue 445 SER 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 412 ASP 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 835 ASN Chi-restraints excluded: chain C residue 838 LYS Chi-restraints excluded: chain C residue 922 THR 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: 1.9990 chunk 246 optimal weight: 9.9990 chunk 249 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** ** 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 = 0.4143 r_free = 0.4143 target = 0.162387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.134428 restraints weight = 38734.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.130793 restraints weight = 59780.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.129168 restraints weight = 53184.391| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22011 Z= 0.201 Angle : 0.651 9.262 29697 Z= 0.337 Chirality : 0.042 0.173 3420 Planarity : 0.004 0.047 3765 Dihedral : 5.035 31.237 2872 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.70 % Favored : 93.22 % Rotamer: Outliers : 2.76 % Allowed : 13.00 % Favored : 84.24 % 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: -0.43 (0.17), residues: 2700 helix: 0.74 (0.15), residues: 1230 sheet: 0.03 (0.30), residues: 303 loop : -1.48 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C1005 HIS 0.005 0.001 HIS A 508 PHE 0.021 0.002 PHE B 684 TYR 0.013 0.002 TYR A 367 ARG 0.004 0.000 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 942) hydrogen bonds : angle 4.61150 ( 2589) covalent geometry : bond 0.00475 (22011) covalent geometry : angle 0.65108 (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 273 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 206 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7438 (pp30) REVERT: B 111 THR cc_start: 0.9405 (m) cc_final: 0.9136 (p) REVERT: B 477 MET cc_start: 0.7675 (mmm) cc_final: 0.7335 (mmt) REVERT: B 886 LEU cc_start: 0.6852 (mm) cc_final: 0.6648 (tp) REVERT: B 963 ASN cc_start: 0.6604 (m-40) cc_final: 0.6340 (t0) REVERT: C 477 MET cc_start: 0.8022 (mmt) cc_final: 0.7232 (mmt) REVERT: C 556 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7024 (mt-10) REVERT: C 881 LEU cc_start: 0.7686 (tp) cc_final: 0.7416 (tt) REVERT: C 917 TRP cc_start: 0.4115 (p90) cc_final: 0.2638 (p90) REVERT: C 1005 TRP cc_start: 0.7970 (m-10) cc_final: 0.7688 (m-10) outliers start: 67 outliers final: 52 residues processed: 254 average time/residue: 0.2909 time to fit residues: 120.6086 Evaluate side-chains 244 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 2.706 ------------------------------------------------------------------------------- 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 170 GLU Chi-restraints excluded: chain A residue 217 CYS 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 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 258 CYS 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 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 549 ILE Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 902 HIS Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 931 PHE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 154 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 192 optimal weight: 0.0040 chunk 212 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 186 optimal weight: 0.9980 overall best weight: 1.1196 ------------------------------------------------------------------------------- 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 908 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 C 963 ASN 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 = 0.163530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.131941 restraints weight = 38904.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.126300 restraints weight = 59735.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.125218 restraints weight = 52597.253| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22011 Z= 0.146 Angle : 0.610 11.612 29697 Z= 0.316 Chirality : 0.041 0.169 3420 Planarity : 0.004 0.041 3765 Dihedral : 4.923 34.037 2872 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.67 % Favored : 93.26 % Rotamer: Outliers : 2.97 % Allowed : 13.90 % Favored : 83.13 % 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: -0.37 (0.17), residues: 2700 helix: 0.88 (0.15), residues: 1230 sheet: -0.08 (0.30), residues: 303 loop : -1.54 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C1005 HIS 0.006 0.001 HIS C 731 PHE 0.048 0.001 PHE B 684 TYR 0.019 0.001 TYR B 594 ARG 0.004 0.000 ARG B 691 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 942) hydrogen bonds : angle 4.46194 ( 2589) covalent geometry : bond 0.00338 (22011) covalent geometry : angle 0.61034 (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 280 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 208 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7398 (pp30) REVERT: B 111 THR cc_start: 0.9375 (m) cc_final: 0.9127 (p) REVERT: B 477 MET cc_start: 0.7644 (mmm) cc_final: 0.7284 (mmt) REVERT: B 611 PHE cc_start: 0.7545 (m-80) cc_final: 0.7332 (t80) REVERT: B 963 ASN cc_start: 0.6608 (m-40) cc_final: 0.6315 (t0) REVERT: C 339 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8406 (tt) REVERT: C 477 MET cc_start: 0.8039 (mmt) cc_final: 0.7231 (mmt) REVERT: C 556 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6991 (mt-10) REVERT: C 881 LEU cc_start: 0.7922 (tp) cc_final: 0.7608 (tt) REVERT: C 917 TRP cc_start: 0.4139 (p90) cc_final: 0.2618 (p90) REVERT: C 1007 PHE cc_start: 0.8052 (m-10) cc_final: 0.7848 (m-10) outliers start: 72 outliers final: 47 residues processed: 261 average time/residue: 0.2923 time to fit residues: 125.2874 Evaluate side-chains 236 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 187 time to evaluate : 2.543 ------------------------------------------------------------------------------- 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 171 SER Chi-restraints excluded: chain A residue 217 CYS 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 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 963 ASN Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 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 218 ASP Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 412 ASP 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 828 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 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: 6.9990 chunk 168 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 199 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 chunk 95 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 257 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** ** 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 963 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.163743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.132478 restraints weight = 38923.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.127718 restraints weight = 57871.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.125649 restraints weight = 52501.567| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22011 Z= 0.142 Angle : 0.629 11.737 29697 Z= 0.321 Chirality : 0.041 0.175 3420 Planarity : 0.004 0.044 3765 Dihedral : 4.865 32.098 2872 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.67 % Favored : 93.26 % Rotamer: Outliers : 2.72 % Allowed : 14.40 % Favored : 82.88 % 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: -0.34 (0.17), residues: 2700 helix: 0.94 (0.16), residues: 1230 sheet: -0.16 (0.30), residues: 303 loop : -1.53 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C1005 HIS 0.024 0.001 HIS C 869 PHE 0.042 0.001 PHE B 684 TYR 0.012 0.001 TYR A 594 ARG 0.004 0.000 ARG B 691 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 942) hydrogen bonds : angle 4.43481 ( 2589) covalent geometry : bond 0.00328 (22011) covalent geometry : angle 0.62910 (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 266 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 200 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7442 (pp30) REVERT: B 111 THR cc_start: 0.9364 (m) cc_final: 0.9134 (p) REVERT: B 477 MET cc_start: 0.7639 (mmm) cc_final: 0.7262 (mmt) REVERT: B 963 ASN cc_start: 0.6583 (m-40) cc_final: 0.6295 (t0) REVERT: C 274 MET cc_start: 0.7933 (mtp) cc_final: 0.7708 (mtp) REVERT: C 339 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8225 (tt) REVERT: C 477 MET cc_start: 0.8026 (mmt) cc_final: 0.7197 (mmt) REVERT: C 556 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7022 (mt-10) REVERT: C 793 MET cc_start: 0.5967 (tpp) cc_final: 0.5746 (tpp) REVERT: C 881 LEU cc_start: 0.7861 (tp) cc_final: 0.7573 (tt) REVERT: C 912 LEU cc_start: 0.7223 (tt) cc_final: 0.6121 (mt) REVERT: C 917 TRP cc_start: 0.3998 (p90) cc_final: 0.2542 (p90) outliers start: 66 outliers final: 50 residues processed: 249 average time/residue: 0.2947 time to fit residues: 122.1843 Evaluate side-chains 239 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 2.516 ------------------------------------------------------------------------------- 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 171 SER 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 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 599 PHE 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 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 218 ASP 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 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 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: 2.9990 chunk 140 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 204 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 601 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.161130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130061 restraints weight = 38806.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.128677 restraints weight = 68897.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.127869 restraints weight = 57162.653| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22011 Z= 0.214 Angle : 0.700 12.910 29697 Z= 0.355 Chirality : 0.043 0.180 3420 Planarity : 0.004 0.043 3765 Dihedral : 5.074 32.411 2871 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.37 % Favored : 92.56 % Rotamer: Outliers : 2.64 % Allowed : 14.85 % Favored : 82.51 % 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: -0.60 (0.17), residues: 2700 helix: 0.74 (0.15), residues: 1239 sheet: -0.29 (0.30), residues: 303 loop : -1.70 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C1005 HIS 0.007 0.001 HIS C 869 PHE 0.058 0.002 PHE B 684 TYR 0.034 0.002 TYR B 679 ARG 0.008 0.001 ARG C 691 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 942) hydrogen bonds : angle 4.65232 ( 2589) covalent geometry : bond 0.00508 (22011) covalent geometry : angle 0.69995 (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 263 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 199 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7405 (pp30) REVERT: A 958 MET cc_start: 0.6807 (mmm) cc_final: 0.5948 (mmm) REVERT: B 477 MET cc_start: 0.7693 (mmm) cc_final: 0.7321 (mmt) REVERT: C 274 MET cc_start: 0.7944 (mtp) cc_final: 0.7728 (mtp) REVERT: C 339 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8463 (tt) REVERT: C 477 MET cc_start: 0.8006 (mmt) cc_final: 0.7130 (mmt) REVERT: C 556 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7027 (mt-10) REVERT: C 793 MET cc_start: 0.6115 (tpp) cc_final: 0.5907 (tpp) REVERT: C 881 LEU cc_start: 0.7850 (tp) cc_final: 0.7582 (tt) REVERT: C 912 LEU cc_start: 0.6878 (tt) cc_final: 0.5599 (mt) REVERT: C 917 TRP cc_start: 0.4323 (p90) cc_final: 0.3892 (p90) outliers start: 64 outliers final: 54 residues processed: 250 average time/residue: 0.2970 time to fit residues: 123.4928 Evaluate side-chains 249 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 2.590 ------------------------------------------------------------------------------- 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 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 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 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 823 GLU 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 A residue 963 ASN 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 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 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 370 LEU Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 825 ILE Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 931 PHE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 176 optimal weight: 0.7980 chunk 185 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 192 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 242 optimal weight: 7.9990 chunk 256 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 845 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 963 ASN C 657 GLN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.163667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.139814 restraints weight = 38801.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.135703 restraints weight = 54853.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.132924 restraints weight = 49754.261| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22011 Z= 0.123 Angle : 0.646 15.850 29697 Z= 0.326 Chirality : 0.041 0.173 3420 Planarity : 0.004 0.044 3765 Dihedral : 4.906 33.778 2871 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 2.23 % Allowed : 15.80 % Favored : 81.97 % 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: -0.48 (0.17), residues: 2700 helix: 0.84 (0.15), residues: 1245 sheet: -0.33 (0.29), residues: 318 loop : -1.64 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 917 HIS 0.008 0.001 HIS C 731 PHE 0.058 0.001 PHE B 684 TYR 0.036 0.001 TYR B 679 ARG 0.009 0.000 ARG C 691 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 942) hydrogen bonds : angle 4.44991 ( 2589) covalent geometry : bond 0.00275 (22011) covalent geometry : angle 0.64589 (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 261 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7211 (pp30) REVERT: A 958 MET cc_start: 0.6504 (mmm) cc_final: 0.5591 (mmm) REVERT: B 111 THR cc_start: 0.9313 (m) cc_final: 0.9086 (p) REVERT: B 477 MET cc_start: 0.7701 (mmm) cc_final: 0.7333 (mmt) REVERT: C 339 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8204 (tt) REVERT: C 477 MET cc_start: 0.8016 (mmt) cc_final: 0.7105 (mmt) REVERT: C 556 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6958 (mt-10) REVERT: C 881 LEU cc_start: 0.7699 (tp) cc_final: 0.7469 (tt) REVERT: C 912 LEU cc_start: 0.6612 (tt) cc_final: 0.5591 (mt) REVERT: C 917 TRP cc_start: 0.4167 (p90) cc_final: 0.3938 (p90) outliers start: 54 outliers final: 43 residues processed: 251 average time/residue: 0.3070 time to fit residues: 127.0888 Evaluate side-chains 232 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 2.616 ------------------------------------------------------------------------------- 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 170 GLU 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 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 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 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 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 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: 0.9980 chunk 127 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ** 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 = 0.4144 r_free = 0.4144 target = 0.162456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.134197 restraints weight = 38044.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.130683 restraints weight = 58404.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129450 restraints weight = 50669.937| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22011 Z= 0.151 Angle : 0.652 14.390 29697 Z= 0.331 Chirality : 0.041 0.189 3420 Planarity : 0.004 0.047 3765 Dihedral : 4.853 31.093 2871 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.04 % Favored : 92.85 % Rotamer: Outliers : 2.10 % Allowed : 15.76 % Favored : 82.14 % 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: -0.54 (0.17), residues: 2700 helix: 0.83 (0.15), residues: 1245 sheet: -0.60 (0.29), residues: 336 loop : -1.65 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 917 HIS 0.021 0.001 HIS B 731 PHE 0.055 0.002 PHE B 684 TYR 0.027 0.001 TYR B 679 ARG 0.008 0.000 ARG C 691 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 942) hydrogen bonds : angle 4.48561 ( 2589) covalent geometry : bond 0.00352 (22011) covalent geometry : angle 0.65158 (29697) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7163.77 seconds wall clock time: 127 minutes 17.66 seconds (7637.66 seconds total)