Starting phenix.real_space_refine on Thu Mar 5 11:13:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fw9_29498/03_2026/8fw9_29498_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fw9_29498/03_2026/8fw9_29498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fw9_29498/03_2026/8fw9_29498_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fw9_29498/03_2026/8fw9_29498_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fw9_29498/03_2026/8fw9_29498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fw9_29498/03_2026/8fw9_29498.map" } resolution = 4.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 101 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21612 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7204 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Chain: "B" Number of atoms: 7204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7204 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Chain: "C" Number of atoms: 7204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7204 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Time building chain proxies: 5.44, per 1000 atoms: 0.25 Number of scatterers: 21612 At special positions: 0 Unit cell: (163.056, 199.08, 95.748, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4017 8.00 N 3660 7.00 C 13824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.1 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: 134 helices and 20 sheets defined 48.3% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 94 through 109 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 157 through 161 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 230 through 240 removed outlier: 4.070A pdb=" N ALA A 234 " --> pdb=" O GLN A 230 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 258 through 267 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 329 through 335 removed outlier: 4.010A pdb=" N ASN A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 358 through 374 removed outlier: 3.729A 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 404 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 498 removed outlier: 3.574A pdb=" N SER A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 511 Processing helix chain 'A' and resid 541 through 565 Processing helix chain 'A' and resid 573 through 580 removed outlier: 3.806A pdb=" N ALA A 577 " --> pdb=" O GLN A 573 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 578 " --> pdb=" O GLU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 602 removed outlier: 3.546A 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: 3.598A pdb=" N VAL A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 686 Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 725 through 735 Processing helix chain 'A' and resid 779 through 789 removed outlier: 3.994A pdb=" N ASN A 789 " --> pdb=" O GLU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 815 Processing helix chain 'A' and resid 833 through 843 Processing helix chain 'A' and resid 863 through 873 removed outlier: 3.516A pdb=" N ALA A 867 " --> pdb=" O ASP A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 894 Processing helix chain 'A' and resid 895 through 904 removed outlier: 3.803A pdb=" N LEU A 900 " --> pdb=" O LEU A 896 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 901 " --> pdb=" O SER A 897 " (cutoff:3.500A) removed outlier: 4.304A 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 980 through 993 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 157 through 161 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 231 through 240 removed outlier: 4.359A pdb=" N ARG B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 258 through 267 Processing helix chain 'B' and resid 268 through 271 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 342 through 347 removed outlier: 3.547A pdb=" N ALA B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 374 Processing helix chain 'B' and resid 375 through 378 Processing helix chain 'B' and resid 382 through 403 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 498 removed outlier: 3.608A pdb=" N SER B 498 " --> pdb=" O THR B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 512 Processing helix chain 'B' and resid 541 through 564 Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.713A pdb=" N PHE B 578 " --> pdb=" O GLU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 602 removed outlier: 3.999A pdb=" N ASP B 597 " --> pdb=" O ASP B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 609 Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.537A pdb=" N VAL B 649 " --> pdb=" O PRO B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 686 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 788 Processing helix chain 'B' and resid 807 through 815 Processing helix chain 'B' and resid 833 through 844 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: 3.623A pdb=" N LEU B 900 " --> pdb=" O LEU B 896 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS B 901 " --> pdb=" O SER B 897 " (cutoff:3.500A) removed outlier: 4.356A 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 980 through 993 Processing helix chain 'B' and resid 1008 through 1013 Processing helix chain 'C' and resid 95 through 109 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 157 through 161 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 230 through 240 removed outlier: 4.444A pdb=" N ALA C 234 " --> pdb=" O GLN C 230 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 253 Processing helix chain 'C' and resid 258 through 267 removed outlier: 3.508A pdb=" N GLU C 262 " --> pdb=" O CYS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 271 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 301 through 312 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 345 removed outlier: 3.532A pdb=" N CYS C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 374 removed outlier: 3.739A 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 403 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 498 removed outlier: 3.679A pdb=" N SER C 498 " --> pdb=" O THR C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 511 Processing helix chain 'C' and resid 541 through 565 Processing helix chain 'C' and resid 573 through 580 removed outlier: 3.697A pdb=" N ALA C 577 " --> pdb=" O GLN C 573 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 578 " --> pdb=" O GLU C 574 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE C 579 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 removed outlier: 4.255A 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: 3.573A pdb=" N VAL C 649 " --> pdb=" O PRO C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 686 removed outlier: 3.754A pdb=" N SER C 686 " --> pdb=" O LYS C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 709 Processing helix chain 'C' and resid 725 through 735 Processing helix chain 'C' and resid 778 through 788 removed outlier: 4.229A pdb=" N LYS C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 815 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: 3.559A pdb=" N LEU C 900 " --> pdb=" O LEU C 896 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS C 901 " --> pdb=" O SER C 897 " (cutoff:3.500A) removed outlier: 4.389A 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 980 through 993 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 151 through 153 Processing sheet with id=AA3, first strand: chain 'A' and resid 427 through 430 Processing sheet with id=AA4, first strand: chain 'A' and resid 583 through 587 removed outlier: 6.062A pdb=" N ILE A 612 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR A 665 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 614 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU A 662 " --> pdb=" O ARG A 691 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLN A 693 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 664 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LYS A 695 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU A 666 " --> pdb=" O LYS A 695 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU A 690 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N MET A 718 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 692 " --> pdb=" O MET A 718 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLU A 720 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 694 " --> pdb=" O GLU A 720 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU A 768 " --> pdb=" O HIS A 797 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N THR A 799 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET A 770 " --> pdb=" O THR A 799 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE A 796 " --> pdb=" O GLN A 826 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL A 828 " --> pdb=" O PHE A 796 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU A 798 " --> pdb=" O VAL A 828 " (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 886 removed outlier: 3.561A pdb=" N LEU A 884 " --> pdb=" O LYS A 911 " (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 151 through 153 Processing sheet with id=AA9, first strand: chain 'B' and resid 427 through 430 Processing sheet with id=AB1, first strand: chain 'B' and resid 583 through 587 removed outlier: 6.724A pdb=" N ARG B 660 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N THR B 688 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 10.147A pdb=" N SER B 716 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU B 690 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N MET B 718 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU B 692 " --> pdb=" O MET B 718 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N GLU B 720 " --> pdb=" O LEU B 692 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE B 694 " --> pdb=" O GLU B 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 801 " --> pdb=" O ASN B 772 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE B 796 " --> pdb=" O GLN B 826 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL B 828 " --> pdb=" O PHE B 796 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 798 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 859 through 860 Processing sheet with id=AB3, first strand: chain 'B' and resid 884 through 885 removed outlier: 7.326A pdb=" N LEU B 884 " --> pdb=" O GLY B 913 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN B 943 " --> pdb=" O LEU B 912 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1000 through 1001 removed outlier: 8.094A pdb=" N ALA B1000 " --> pdb=" O VAL B1022 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AB6, first strand: chain 'C' and resid 151 through 153 removed outlier: 6.472A pdb=" N CYS C 165 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N THR C 279 " --> pdb=" O CYS C 165 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE C 167 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 427 through 430 Processing sheet with id=AB8, first strand: chain 'C' and resid 583 through 587 removed outlier: 6.250A pdb=" N LEU C 662 " --> pdb=" O ARG C 691 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLN C 693 " --> pdb=" O LEU C 662 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 664 " --> pdb=" O GLN C 693 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU C 690 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 716 " --> pdb=" O LEU C 690 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 859 through 860 Processing sheet with id=AC1, first strand: chain 'C' and resid 884 through 885 removed outlier: 7.209A pdb=" N LEU C 884 " --> pdb=" O GLY C 913 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN C 943 " --> pdb=" O LEU C 912 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1000 through 1001 removed outlier: 8.053A pdb=" N ALA C1000 " --> pdb=" O VAL C1022 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 931 hydrogen bonds defined for protein. 2601 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: 5.04 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3684 1.31 - 1.44: 5530 1.44 - 1.57: 12627 1.57 - 1.71: 8 1.71 - 1.84: 162 Bond restraints: 22011 Sorted by residual: bond pdb=" N ALA A 307 " pdb=" CA ALA A 307 " ideal model delta sigma weight residual 1.459 1.412 0.047 1.21e-02 6.83e+03 1.49e+01 bond pdb=" CD GLU A 729 " pdb=" OE1 GLU A 729 " ideal model delta sigma weight residual 1.249 1.176 0.073 1.90e-02 2.77e+03 1.46e+01 bond pdb=" CD GLU A 729 " pdb=" OE2 GLU A 729 " ideal model delta sigma weight residual 1.249 1.177 0.072 1.90e-02 2.77e+03 1.43e+01 bond pdb=" CB ILE C 644 " pdb=" CG1 ILE C 644 " ideal model delta sigma weight residual 1.530 1.604 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" N ALA A 548 " pdb=" CA ALA A 548 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.21e-02 6.83e+03 1.26e+01 ... (remaining 22006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 28330 2.41 - 4.83: 1167 4.83 - 7.24: 180 7.24 - 9.66: 15 9.66 - 12.07: 5 Bond angle restraints: 29697 Sorted by residual: angle pdb=" C ILE B 223 " pdb=" N PRO B 224 " pdb=" CA PRO B 224 " ideal model delta sigma weight residual 119.89 128.09 -8.20 1.02e+00 9.61e-01 6.46e+01 angle pdb=" C LYS B 254 " pdb=" N PRO B 255 " pdb=" CA PRO B 255 " ideal model delta sigma weight residual 119.56 127.51 -7.95 1.02e+00 9.61e-01 6.07e+01 angle pdb=" C GLU A 818 " pdb=" N PRO A 819 " pdb=" CA PRO A 819 " ideal model delta sigma weight residual 119.90 127.65 -7.75 1.02e+00 9.61e-01 5.77e+01 angle pdb=" C LEU A 602 " pdb=" N PRO A 603 " pdb=" CA PRO A 603 " ideal model delta sigma weight residual 120.03 127.36 -7.33 9.90e-01 1.02e+00 5.48e+01 angle pdb=" C ILE A 591 " pdb=" N PRO A 592 " pdb=" CA PRO A 592 " ideal model delta sigma weight residual 119.78 127.22 -7.44 1.03e+00 9.43e-01 5.22e+01 ... (remaining 29692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 12771 17.37 - 34.74: 409 34.74 - 52.10: 76 52.10 - 69.47: 37 69.47 - 86.84: 24 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 -142.63 -37.37 0 5.00e+00 4.00e-02 5.59e+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 -144.66 -35.34 0 5.00e+00 4.00e-02 5.00e+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 -146.31 -33.69 0 5.00e+00 4.00e-02 4.54e+01 ... (remaining 13314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2339 0.065 - 0.129: 798 0.129 - 0.194: 254 0.194 - 0.258: 24 0.258 - 0.323: 5 Chirality restraints: 3420 Sorted by residual: chirality pdb=" CA ALA A 307 " pdb=" N ALA A 307 " pdb=" C ALA A 307 " pdb=" CB ALA A 307 " both_signs ideal model delta sigma weight residual False 2.48 2.16 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA ALA A 548 " pdb=" N ALA A 548 " pdb=" C ALA A 548 " pdb=" CB ALA A 548 " both_signs ideal model delta sigma weight residual False 2.48 2.77 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ILE C 223 " pdb=" N ILE C 223 " pdb=" C ILE C 223 " pdb=" CB ILE C 223 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 3417 not shown) Planarity restraints: 3765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B1024 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ALA B1024 " 0.063 2.00e-02 2.50e+03 pdb=" O ALA B1024 " -0.022 2.00e-02 2.50e+03 pdb=" OXT ALA B1024 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 954 " 0.034 2.00e-02 2.50e+03 1.82e-02 8.30e+00 pdb=" CG TRP C 954 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP C 954 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP C 954 " -0.031 2.00e-02 2.50e+03 pdb=" NE1 TRP C 954 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 954 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP C 954 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 954 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 954 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP C 954 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 917 " 0.034 2.00e-02 2.50e+03 1.75e-02 7.69e+00 pdb=" CG TRP A 917 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 917 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 917 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 917 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 917 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 917 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 917 " 0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 917 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 917 " 0.010 2.00e-02 2.50e+03 ... (remaining 3762 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 7239 2.84 - 3.36: 20986 3.36 - 3.87: 35034 3.87 - 4.39: 42648 4.39 - 4.90: 67836 Nonbonded interactions: 173743 Sorted by model distance: nonbonded pdb=" OG SER A 485 " pdb=" N THR A 486 " model vdw 2.330 3.120 nonbonded pdb=" OG SER B 485 " pdb=" N THR B 486 " model vdw 2.347 3.120 nonbonded pdb=" NZ LYS C 175 " pdb=" OD2 ASP C 248 " model vdw 2.354 3.120 nonbonded pdb=" O SER A 481 " pdb=" OG SER A 485 " model vdw 2.356 3.040 nonbonded pdb=" O SER B 481 " pdb=" OG SER B 485 " model vdw 2.359 3.040 ... (remaining 173738 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: 0.03 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: 10.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 23.110 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.085 22011 Z= 0.647 Angle : 1.195 12.072 29697 Z= 0.825 Chirality : 0.070 0.323 3420 Planarity : 0.005 0.036 3765 Dihedral : 10.840 86.838 8187 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.07 % Favored : 94.07 % Rotamer: Outliers : 0.08 % Allowed : 0.66 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.16), residues: 2700 helix: -0.15 (0.14), residues: 1206 sheet: -0.22 (0.27), residues: 339 loop : -0.94 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 526 TYR 0.031 0.004 TYR B 449 PHE 0.020 0.003 PHE C 957 TRP 0.034 0.007 TRP A 917 HIS 0.004 0.001 HIS A 797 Details of bonding type rmsd covalent geometry : bond 0.01173 (22011) covalent geometry : angle 1.19483 (29697) hydrogen bonds : bond 0.17694 ( 931) hydrogen bonds : angle 6.99691 ( 2601) *********************** 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 650 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 648 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.9586 (tp) cc_final: 0.9186 (tp) REVERT: A 223 ILE cc_start: 0.7190 (mt) cc_final: 0.6753 (mm) REVERT: A 232 PHE cc_start: 0.9100 (t80) cc_final: 0.8867 (t80) REVERT: A 233 MET cc_start: 0.9093 (mmt) cc_final: 0.8280 (mmm) REVERT: A 353 GLU cc_start: 0.8056 (tp30) cc_final: 0.7559 (mp0) REVERT: A 408 PHE cc_start: 0.8728 (m-80) cc_final: 0.8418 (m-10) REVERT: A 513 TYR cc_start: 0.7704 (p90) cc_final: 0.7321 (p90) REVERT: A 584 LEU cc_start: 0.9252 (tp) cc_final: 0.9043 (tt) REVERT: A 659 PHE cc_start: 0.8894 (m-80) cc_final: 0.8434 (m-10) REVERT: A 716 SER cc_start: 0.9137 (t) cc_final: 0.8302 (m) REVERT: A 793 MET cc_start: 0.6809 (mmm) cc_final: 0.6586 (mmm) REVERT: A 831 CYS cc_start: 0.8325 (m) cc_final: 0.8015 (m) REVERT: A 941 GLN cc_start: 0.8127 (mp10) cc_final: 0.7662 (mm-40) REVERT: B 197 PHE cc_start: 0.8763 (m-80) cc_final: 0.8467 (m-10) REVERT: B 220 LEU cc_start: 0.9250 (mt) cc_final: 0.9000 (mt) REVERT: B 241 GLN cc_start: 0.8127 (mt0) cc_final: 0.7889 (pm20) REVERT: B 574 GLU cc_start: 0.8591 (mp0) cc_final: 0.8178 (mp0) REVERT: B 729 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8545 (tp30) REVERT: B 768 LEU cc_start: 0.9119 (tp) cc_final: 0.8724 (tp) REVERT: B 770 MET cc_start: 0.7500 (tmm) cc_final: 0.7067 (tmm) REVERT: B 796 PHE cc_start: 0.8730 (t80) cc_final: 0.8455 (t80) REVERT: B 885 MET cc_start: 0.6965 (mmp) cc_final: 0.6653 (mmp) REVERT: B 954 TRP cc_start: 0.7003 (m-90) cc_final: 0.6451 (m-90) REVERT: B 1002 LEU cc_start: 0.9137 (tp) cc_final: 0.8139 (tp) REVERT: B 1005 TRP cc_start: 0.8175 (m100) cc_final: 0.7169 (m100) REVERT: B 1008 ASP cc_start: 0.9284 (t0) cc_final: 0.8985 (m-30) REVERT: C 106 LYS cc_start: 0.9020 (mttt) cc_final: 0.8606 (mmmt) REVERT: C 115 LEU cc_start: 0.9158 (mt) cc_final: 0.8776 (mm) REVERT: C 122 GLU cc_start: 0.8148 (mp0) cc_final: 0.7869 (tp30) REVERT: C 212 LEU cc_start: 0.9231 (tp) cc_final: 0.8651 (tp) REVERT: C 244 LEU cc_start: 0.9244 (mt) cc_final: 0.8853 (mp) REVERT: C 571 LEU cc_start: 0.9482 (mt) cc_final: 0.9274 (mm) REVERT: C 585 TYR cc_start: 0.8885 (t80) cc_final: 0.8109 (t80) REVERT: C 615 ASP cc_start: 0.8211 (t0) cc_final: 0.7774 (m-30) REVERT: C 792 LYS cc_start: 0.7283 (mttt) cc_final: 0.6940 (ttpp) REVERT: C 823 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7296 (mm-30) REVERT: C 826 GLN cc_start: 0.7690 (mt0) cc_final: 0.7436 (tp40) outliers start: 2 outliers final: 1 residues processed: 650 average time/residue: 0.1641 time to fit residues: 159.4512 Evaluate side-chains 331 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 330 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 ASN A 749 GLN A 797 HIS A 800 HIS ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 HIS ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN B 155 ASN B 162 GLN B 268 ASN B 789 ASN ** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS C 268 ASN ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 HIS C 908 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.084174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.063225 restraints weight = 112925.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.065296 restraints weight = 66640.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.066716 restraints weight = 46191.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.067678 restraints weight = 35521.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.068379 restraints weight = 29480.560| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22011 Z= 0.142 Angle : 0.649 12.383 29697 Z= 0.344 Chirality : 0.040 0.200 3420 Planarity : 0.004 0.060 3765 Dihedral : 4.948 41.166 2871 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.22 % Rotamer: Outliers : 0.17 % Allowed : 1.94 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 4.55 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.17), residues: 2700 helix: 1.16 (0.15), residues: 1164 sheet: 0.11 (0.28), residues: 309 loop : -1.12 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 691 TYR 0.018 0.001 TYR A 487 PHE 0.024 0.002 PHE B 957 TRP 0.026 0.002 TRP A 186 HIS 0.005 0.001 HIS A 744 Details of bonding type rmsd covalent geometry : bond 0.00303 (22011) covalent geometry : angle 0.64923 (29697) hydrogen bonds : bond 0.04551 ( 931) hydrogen bonds : angle 5.02685 ( 2601) *********************** 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 436 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 432 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8841 (tmm) cc_final: 0.8548 (tmm) REVERT: A 233 MET cc_start: 0.8876 (mmt) cc_final: 0.8171 (mmm) REVERT: A 309 ILE cc_start: 0.9541 (mt) cc_final: 0.9265 (tp) REVERT: A 321 LEU cc_start: 0.9100 (tp) cc_final: 0.8888 (tt) REVERT: A 503 ARG cc_start: 0.9160 (mtp85) cc_final: 0.8926 (mtp85) REVERT: A 513 TYR cc_start: 0.7064 (p90) cc_final: 0.6822 (p90) REVERT: A 571 LEU cc_start: 0.9346 (mm) cc_final: 0.9137 (mm) REVERT: A 755 LEU cc_start: 0.9170 (pp) cc_final: 0.8804 (tt) REVERT: A 793 MET cc_start: 0.6722 (mmm) cc_final: 0.6127 (mmm) REVERT: B 114 PHE cc_start: 0.8198 (t80) cc_final: 0.7979 (t80) REVERT: B 185 LEU cc_start: 0.9595 (mt) cc_final: 0.8994 (mt) REVERT: B 197 PHE cc_start: 0.8579 (m-80) cc_final: 0.7763 (m-10) REVERT: B 274 MET cc_start: 0.8165 (mmm) cc_final: 0.7693 (mmm) REVERT: B 321 LEU cc_start: 0.9320 (mt) cc_final: 0.8947 (tt) REVERT: B 480 ILE cc_start: 0.9092 (mm) cc_final: 0.8718 (tt) REVERT: B 584 LEU cc_start: 0.9304 (tp) cc_final: 0.9049 (tp) REVERT: B 680 LEU cc_start: 0.9293 (mt) cc_final: 0.9047 (mt) REVERT: B 694 ILE cc_start: 0.9472 (mp) cc_final: 0.9249 (tt) REVERT: B 732 ILE cc_start: 0.8808 (mt) cc_final: 0.8566 (pt) REVERT: B 770 MET cc_start: 0.6983 (tmm) cc_final: 0.6517 (tmm) REVERT: B 796 PHE cc_start: 0.8832 (t80) cc_final: 0.8601 (t80) REVERT: B 808 MET cc_start: 0.5885 (mtt) cc_final: 0.4459 (mpp) REVERT: B 1005 TRP cc_start: 0.8271 (m100) cc_final: 0.7436 (m100) REVERT: C 106 LYS cc_start: 0.9221 (mttt) cc_final: 0.8681 (mmmt) REVERT: C 122 GLU cc_start: 0.8136 (mp0) cc_final: 0.7864 (tp30) REVERT: C 215 THR cc_start: 0.9279 (m) cc_final: 0.9031 (p) REVERT: C 220 LEU cc_start: 0.8980 (mt) cc_final: 0.8775 (mt) REVERT: C 248 ASP cc_start: 0.8435 (t0) cc_final: 0.8050 (t0) REVERT: C 337 THR cc_start: 0.9113 (m) cc_final: 0.8778 (p) REVERT: C 401 VAL cc_start: 0.9444 (t) cc_final: 0.9151 (t) REVERT: C 487 TYR cc_start: 0.8446 (m-80) cc_final: 0.7850 (m-80) REVERT: C 597 ASP cc_start: 0.9293 (m-30) cc_final: 0.9086 (m-30) REVERT: C 765 LEU cc_start: 0.8032 (tp) cc_final: 0.7797 (tp) REVERT: C 792 LYS cc_start: 0.7392 (mttt) cc_final: 0.7081 (ttpt) REVERT: C 998 GLN cc_start: 0.9217 (pm20) cc_final: 0.8977 (pm20) outliers start: 4 outliers final: 0 residues processed: 435 average time/residue: 0.1416 time to fit residues: 97.8835 Evaluate side-chains 287 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 25 optimal weight: 0.8980 chunk 199 optimal weight: 0.4980 chunk 249 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 64 optimal weight: 0.0030 chunk 143 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 134 optimal weight: 30.0000 chunk 192 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 ASN A 348 GLN A 357 HIS A 374 ASN A 675 GLN A 744 HIS ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 162 GLN B 865 ASN C 147 HIS ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.084449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.063460 restraints weight = 112680.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.065511 restraints weight = 66328.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.066930 restraints weight = 46028.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.067891 restraints weight = 35469.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.068574 restraints weight = 29455.609| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22011 Z= 0.118 Angle : 0.605 12.142 29697 Z= 0.317 Chirality : 0.040 0.180 3420 Planarity : 0.004 0.054 3765 Dihedral : 4.764 33.960 2871 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.03 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2700 helix: 1.27 (0.16), residues: 1182 sheet: 0.16 (0.28), residues: 306 loop : -1.13 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 242 TYR 0.014 0.001 TYR C 594 PHE 0.026 0.002 PHE B 957 TRP 0.016 0.001 TRP A 917 HIS 0.015 0.001 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00248 (22011) covalent geometry : angle 0.60536 (29697) hydrogen bonds : bond 0.03670 ( 931) hydrogen bonds : angle 4.60476 ( 2601) *********************** 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 398 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 95 GLU cc_start: 0.7731 (pp20) cc_final: 0.7530 (pm20) REVERT: A 184 MET cc_start: 0.8767 (tmm) cc_final: 0.8557 (tmm) REVERT: A 233 MET cc_start: 0.8680 (mmt) cc_final: 0.7412 (mmt) REVERT: A 309 ILE cc_start: 0.9569 (mt) cc_final: 0.9332 (tp) REVERT: A 321 LEU cc_start: 0.9084 (tp) cc_final: 0.8812 (tt) REVERT: A 408 PHE cc_start: 0.8642 (m-80) cc_final: 0.8397 (m-10) REVERT: A 503 ARG cc_start: 0.9112 (mtp85) cc_final: 0.8880 (mtp85) REVERT: A 513 TYR cc_start: 0.7037 (p90) cc_final: 0.6822 (p90) REVERT: A 599 PHE cc_start: 0.8910 (m-80) cc_final: 0.8623 (m-80) REVERT: A 755 LEU cc_start: 0.9113 (pp) cc_final: 0.8831 (tt) REVERT: A 793 MET cc_start: 0.6519 (mmm) cc_final: 0.6222 (mmm) REVERT: B 158 LEU cc_start: 0.8845 (mt) cc_final: 0.8416 (tp) REVERT: B 185 LEU cc_start: 0.9601 (mt) cc_final: 0.9388 (mt) REVERT: B 274 MET cc_start: 0.8229 (mmm) cc_final: 0.7889 (mmm) REVERT: B 321 LEU cc_start: 0.9288 (mt) cc_final: 0.8919 (tt) REVERT: B 732 ILE cc_start: 0.8839 (mt) cc_final: 0.8611 (pt) REVERT: B 808 MET cc_start: 0.5248 (mtt) cc_final: 0.3934 (mpp) REVERT: B 969 PHE cc_start: 0.8717 (p90) cc_final: 0.8486 (p90) REVERT: C 106 LYS cc_start: 0.9344 (mttt) cc_final: 0.8870 (mmmt) REVERT: C 122 GLU cc_start: 0.8109 (mp0) cc_final: 0.7829 (tp30) REVERT: C 184 MET cc_start: 0.8786 (ttm) cc_final: 0.8484 (tpp) REVERT: C 215 THR cc_start: 0.9357 (m) cc_final: 0.9146 (p) REVERT: C 233 MET cc_start: 0.9078 (mpp) cc_final: 0.8800 (mpp) REVERT: C 248 ASP cc_start: 0.8173 (t0) cc_final: 0.7968 (t0) REVERT: C 337 THR cc_start: 0.9076 (m) cc_final: 0.8868 (p) REVERT: C 401 VAL cc_start: 0.9455 (t) cc_final: 0.9142 (t) REVERT: C 473 TYR cc_start: 0.8182 (m-80) cc_final: 0.7889 (m-80) REVERT: C 487 TYR cc_start: 0.8440 (m-80) cc_final: 0.7894 (m-80) REVERT: C 597 ASP cc_start: 0.9190 (m-30) cc_final: 0.8915 (m-30) REVERT: C 792 LYS cc_start: 0.7420 (mttt) cc_final: 0.7001 (ttpt) REVERT: C 970 PHE cc_start: 0.9419 (p90) cc_final: 0.9177 (p90) outliers start: 0 outliers final: 0 residues processed: 398 average time/residue: 0.1409 time to fit residues: 89.5850 Evaluate side-chains 276 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 143 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 92 optimal weight: 0.2980 chunk 121 optimal weight: 5.9990 chunk 196 optimal weight: 0.0570 chunk 263 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 HIS ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 ASN C 604 ASN ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.083416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.062297 restraints weight = 115089.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.064308 restraints weight = 68220.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.065680 restraints weight = 47849.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.066598 restraints weight = 37278.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.067240 restraints weight = 31253.353| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22011 Z= 0.118 Angle : 0.604 11.617 29697 Z= 0.312 Chirality : 0.040 0.198 3420 Planarity : 0.004 0.051 3765 Dihedral : 4.698 32.890 2871 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2700 helix: 1.42 (0.16), residues: 1179 sheet: -0.24 (0.27), residues: 336 loop : -1.19 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 691 TYR 0.015 0.001 TYR C 594 PHE 0.024 0.001 PHE C 957 TRP 0.039 0.002 TRP A 186 HIS 0.008 0.001 HIS A 744 Details of bonding type rmsd covalent geometry : bond 0.00254 (22011) covalent geometry : angle 0.60360 (29697) hydrogen bonds : bond 0.03377 ( 931) hydrogen bonds : angle 4.39278 ( 2601) *********************** 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 349 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7917 (pp20) cc_final: 0.7686 (pm20) REVERT: A 233 MET cc_start: 0.8700 (mmt) cc_final: 0.8061 (mmt) REVERT: A 309 ILE cc_start: 0.9529 (mt) cc_final: 0.9319 (tp) REVERT: A 321 LEU cc_start: 0.9098 (tp) cc_final: 0.8793 (tt) REVERT: A 340 PHE cc_start: 0.9080 (m-10) cc_final: 0.8832 (m-10) REVERT: A 408 PHE cc_start: 0.8739 (m-80) cc_final: 0.8533 (m-10) REVERT: A 503 ARG cc_start: 0.9285 (mtp85) cc_final: 0.8804 (mtp85) REVERT: A 513 TYR cc_start: 0.7066 (p90) cc_final: 0.6847 (p90) REVERT: A 659 PHE cc_start: 0.8707 (m-10) cc_final: 0.8239 (m-10) REVERT: A 755 LEU cc_start: 0.9121 (pp) cc_final: 0.8833 (tt) REVERT: A 793 MET cc_start: 0.6571 (mmm) cc_final: 0.6289 (mmm) REVERT: A 899 LEU cc_start: 0.9343 (mt) cc_final: 0.9098 (mt) REVERT: A 902 HIS cc_start: 0.8201 (p90) cc_final: 0.7620 (t-90) REVERT: B 106 LYS cc_start: 0.9171 (mttt) cc_final: 0.8738 (mmtt) REVERT: B 114 PHE cc_start: 0.8395 (t80) cc_final: 0.8191 (t80) REVERT: B 126 ILE cc_start: 0.9055 (mm) cc_final: 0.8844 (mm) REVERT: B 158 LEU cc_start: 0.8832 (mt) cc_final: 0.8421 (tp) REVERT: B 185 LEU cc_start: 0.9645 (mt) cc_final: 0.9365 (mt) REVERT: B 274 MET cc_start: 0.8188 (mmm) cc_final: 0.7570 (mmm) REVERT: B 321 LEU cc_start: 0.9330 (mt) cc_final: 0.8952 (tt) REVERT: B 732 ILE cc_start: 0.8915 (mt) cc_final: 0.8686 (pt) REVERT: B 770 MET cc_start: 0.6440 (tmm) cc_final: 0.5919 (tmm) REVERT: B 808 MET cc_start: 0.5390 (mtt) cc_final: 0.4131 (mpp) REVERT: B 874 ARG cc_start: 0.8635 (mmp80) cc_final: 0.8331 (mtt180) REVERT: B 994 LEU cc_start: 0.8457 (mt) cc_final: 0.8255 (mt) REVERT: B 1002 LEU cc_start: 0.9180 (tp) cc_final: 0.8403 (tp) REVERT: C 106 LYS cc_start: 0.9379 (mttt) cc_final: 0.8924 (mmmt) REVERT: C 122 GLU cc_start: 0.8093 (mp0) cc_final: 0.7773 (tp30) REVERT: C 184 MET cc_start: 0.8700 (ttm) cc_final: 0.8376 (tpp) REVERT: C 215 THR cc_start: 0.9288 (m) cc_final: 0.9088 (p) REVERT: C 233 MET cc_start: 0.9143 (mpp) cc_final: 0.8940 (mpp) REVERT: C 321 LEU cc_start: 0.9180 (tp) cc_final: 0.8951 (tp) REVERT: C 401 VAL cc_start: 0.9488 (t) cc_final: 0.9216 (t) REVERT: C 473 TYR cc_start: 0.8257 (m-80) cc_final: 0.7936 (m-80) REVERT: C 487 TYR cc_start: 0.8571 (m-80) cc_final: 0.8116 (m-80) REVERT: C 550 ASN cc_start: 0.8948 (m110) cc_final: 0.8538 (m-40) REVERT: C 571 LEU cc_start: 0.9377 (mm) cc_final: 0.9146 (mt) REVERT: C 597 ASP cc_start: 0.9136 (m-30) cc_final: 0.8846 (m-30) REVERT: C 599 PHE cc_start: 0.9283 (m-80) cc_final: 0.8912 (m-80) REVERT: C 765 LEU cc_start: 0.7904 (tp) cc_final: 0.7571 (tp) REVERT: C 792 LYS cc_start: 0.7450 (mttt) cc_final: 0.7083 (ttpt) REVERT: C 875 MET cc_start: 0.8278 (pmm) cc_final: 0.8014 (pmm) REVERT: C 970 PHE cc_start: 0.9465 (p90) cc_final: 0.9099 (p90) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.1328 time to fit residues: 74.9581 Evaluate side-chains 259 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 6 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 169 optimal weight: 0.0980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 HIS ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 ASN B 162 GLN B 219 GLN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 772 ASN C 147 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.084006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.062711 restraints weight = 117374.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.064770 restraints weight = 69605.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.066133 restraints weight = 48811.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.067064 restraints weight = 38317.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.067700 restraints weight = 32220.882| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22011 Z= 0.103 Angle : 0.590 11.360 29697 Z= 0.302 Chirality : 0.040 0.176 3420 Planarity : 0.003 0.045 3765 Dihedral : 4.601 31.007 2871 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2700 helix: 1.40 (0.16), residues: 1197 sheet: -0.24 (0.27), residues: 333 loop : -1.29 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 242 TYR 0.014 0.001 TYR C 594 PHE 0.022 0.001 PHE C 957 TRP 0.031 0.002 TRP B1005 HIS 0.015 0.001 HIS A 744 Details of bonding type rmsd covalent geometry : bond 0.00216 (22011) covalent geometry : angle 0.59031 (29697) hydrogen bonds : bond 0.03103 ( 931) hydrogen bonds : angle 4.20693 ( 2601) *********************** 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 341 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LEU cc_start: 0.9059 (tp) cc_final: 0.8749 (tt) REVERT: A 408 PHE cc_start: 0.8745 (m-80) cc_final: 0.8539 (m-10) REVERT: A 474 LEU cc_start: 0.9389 (tp) cc_final: 0.9174 (pp) REVERT: A 503 ARG cc_start: 0.9234 (mtp85) cc_final: 0.8658 (ttm110) REVERT: A 755 LEU cc_start: 0.9207 (pp) cc_final: 0.8855 (tt) REVERT: A 793 MET cc_start: 0.6553 (mmm) cc_final: 0.6297 (mmm) REVERT: A 831 CYS cc_start: 0.8057 (m) cc_final: 0.7304 (m) REVERT: B 158 LEU cc_start: 0.8906 (mt) cc_final: 0.8452 (tp) REVERT: B 175 LYS cc_start: 0.8296 (tptp) cc_final: 0.7889 (mptt) REVERT: B 197 PHE cc_start: 0.7740 (m-10) cc_final: 0.7459 (m-10) REVERT: B 274 MET cc_start: 0.8027 (mmm) cc_final: 0.7670 (mmm) REVERT: B 321 LEU cc_start: 0.9335 (mt) cc_final: 0.8959 (tt) REVERT: B 732 ILE cc_start: 0.8901 (mt) cc_final: 0.8675 (pt) REVERT: B 770 MET cc_start: 0.6566 (tmm) cc_final: 0.6088 (tmm) REVERT: B 808 MET cc_start: 0.5246 (mtt) cc_final: 0.4050 (mpp) REVERT: B 970 PHE cc_start: 0.7395 (p90) cc_final: 0.6317 (p90) REVERT: B 994 LEU cc_start: 0.8472 (mt) cc_final: 0.8268 (mt) REVERT: B 1002 LEU cc_start: 0.9090 (tp) cc_final: 0.8247 (tp) REVERT: B 1005 TRP cc_start: 0.7613 (m100) cc_final: 0.6878 (m100) REVERT: C 106 LYS cc_start: 0.9394 (mttt) cc_final: 0.8939 (mmmt) REVERT: C 122 GLU cc_start: 0.7923 (mp0) cc_final: 0.7681 (tp30) REVERT: C 321 LEU cc_start: 0.9119 (tp) cc_final: 0.8839 (tp) REVERT: C 401 VAL cc_start: 0.9481 (t) cc_final: 0.9235 (t) REVERT: C 473 TYR cc_start: 0.8172 (m-80) cc_final: 0.7828 (m-80) REVERT: C 487 TYR cc_start: 0.8451 (m-80) cc_final: 0.8064 (m-80) REVERT: C 571 LEU cc_start: 0.9404 (mm) cc_final: 0.9185 (mt) REVERT: C 597 ASP cc_start: 0.9094 (m-30) cc_final: 0.8774 (m-30) REVERT: C 599 PHE cc_start: 0.9179 (m-80) cc_final: 0.8841 (m-80) REVERT: C 718 MET cc_start: 0.8221 (ppp) cc_final: 0.7996 (ppp) REVERT: C 765 LEU cc_start: 0.8021 (tp) cc_final: 0.7719 (tp) REVERT: C 792 LYS cc_start: 0.7385 (mttt) cc_final: 0.7023 (ttpt) REVERT: C 958 MET cc_start: 0.7775 (mmp) cc_final: 0.7470 (mmm) REVERT: C 970 PHE cc_start: 0.9538 (p90) cc_final: 0.9175 (p90) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1289 time to fit residues: 71.4228 Evaluate side-chains 257 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 247 optimal weight: 9.9990 chunk 224 optimal weight: 0.0050 chunk 138 optimal weight: 0.4980 chunk 236 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 128 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS C 550 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.083650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.062481 restraints weight = 117891.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.064468 restraints weight = 71261.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.065804 restraints weight = 50459.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.066692 restraints weight = 39615.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.067320 restraints weight = 33474.073| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22011 Z= 0.103 Angle : 0.589 11.592 29697 Z= 0.299 Chirality : 0.039 0.178 3420 Planarity : 0.003 0.045 3765 Dihedral : 4.500 29.720 2871 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2700 helix: 1.56 (0.16), residues: 1182 sheet: -0.27 (0.28), residues: 333 loop : -1.33 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 691 TYR 0.016 0.001 TYR C 594 PHE 0.026 0.001 PHE B 114 TRP 0.016 0.001 TRP A 186 HIS 0.005 0.001 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00216 (22011) covalent geometry : angle 0.58919 (29697) hydrogen bonds : bond 0.02938 ( 931) hydrogen bonds : angle 4.07609 ( 2601) *********************** 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 333 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 PHE cc_start: 0.8768 (m-80) cc_final: 0.8563 (m-10) REVERT: A 659 PHE cc_start: 0.8573 (m-10) cc_final: 0.8097 (m-10) REVERT: A 755 LEU cc_start: 0.9151 (pp) cc_final: 0.8817 (tt) REVERT: A 793 MET cc_start: 0.6568 (mmm) cc_final: 0.6186 (mmm) REVERT: A 808 MET cc_start: 0.7768 (tmm) cc_final: 0.6784 (ttp) REVERT: A 826 GLN cc_start: 0.8955 (mp10) cc_final: 0.8714 (mp10) REVERT: A 875 MET cc_start: 0.7678 (tmm) cc_final: 0.7457 (mtm) REVERT: A 902 HIS cc_start: 0.8185 (p90) cc_final: 0.7444 (p90) REVERT: A 952 ASP cc_start: 0.8774 (t0) cc_final: 0.8336 (p0) REVERT: B 158 LEU cc_start: 0.8929 (mt) cc_final: 0.8431 (tp) REVERT: B 175 LYS cc_start: 0.8276 (tptp) cc_final: 0.7904 (mptt) REVERT: B 274 MET cc_start: 0.7952 (mmm) cc_final: 0.7707 (mmm) REVERT: B 321 LEU cc_start: 0.9121 (mt) cc_final: 0.8815 (tt) REVERT: B 714 ILE cc_start: 0.8522 (pt) cc_final: 0.8260 (tp) REVERT: B 717 LEU cc_start: 0.9563 (mm) cc_final: 0.9098 (mm) REVERT: B 732 ILE cc_start: 0.8921 (mt) cc_final: 0.8705 (pt) REVERT: B 775 MET cc_start: 0.5709 (mpp) cc_final: 0.5318 (mpp) REVERT: B 808 MET cc_start: 0.5183 (mtt) cc_final: 0.4061 (mpp) REVERT: B 1002 LEU cc_start: 0.9073 (tp) cc_final: 0.8126 (tp) REVERT: B 1005 TRP cc_start: 0.7778 (m100) cc_final: 0.7277 (m100) REVERT: C 106 LYS cc_start: 0.9419 (mttt) cc_final: 0.8949 (mmmt) REVERT: C 184 MET cc_start: 0.8388 (ttt) cc_final: 0.8129 (tpp) REVERT: C 401 VAL cc_start: 0.9502 (t) cc_final: 0.9263 (t) REVERT: C 487 TYR cc_start: 0.8491 (m-80) cc_final: 0.8090 (m-80) REVERT: C 550 ASN cc_start: 0.8922 (m110) cc_final: 0.8510 (m-40) REVERT: C 571 LEU cc_start: 0.9431 (mm) cc_final: 0.9198 (mt) REVERT: C 597 ASP cc_start: 0.9107 (m-30) cc_final: 0.8827 (m-30) REVERT: C 599 PHE cc_start: 0.9230 (m-80) cc_final: 0.8795 (m-80) REVERT: C 718 MET cc_start: 0.8225 (ppp) cc_final: 0.7839 (ppp) REVERT: C 744 HIS cc_start: 0.8561 (m-70) cc_final: 0.8194 (m90) REVERT: C 765 LEU cc_start: 0.8038 (tp) cc_final: 0.7671 (tp) REVERT: C 792 LYS cc_start: 0.7384 (mttt) cc_final: 0.6988 (ttpp) REVERT: C 958 MET cc_start: 0.7900 (mmp) cc_final: 0.7452 (mmm) REVERT: C 970 PHE cc_start: 0.9504 (p90) cc_final: 0.9217 (p90) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.1322 time to fit residues: 71.7098 Evaluate side-chains 249 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 4 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 173 optimal weight: 1.9990 chunk 266 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 268 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 HIS B 162 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.080863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.059765 restraints weight = 117702.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.061637 restraints weight = 71933.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.062919 restraints weight = 51482.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.063777 restraints weight = 40733.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.064383 restraints weight = 34592.856| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22011 Z= 0.155 Angle : 0.641 12.125 29697 Z= 0.329 Chirality : 0.040 0.178 3420 Planarity : 0.004 0.058 3765 Dihedral : 4.749 28.931 2871 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.17), residues: 2700 helix: 1.47 (0.16), residues: 1182 sheet: -0.48 (0.28), residues: 339 loop : -1.33 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 691 TYR 0.017 0.002 TYR C 594 PHE 0.023 0.002 PHE C 957 TRP 0.019 0.002 TRP C 954 HIS 0.011 0.001 HIS A 744 Details of bonding type rmsd covalent geometry : bond 0.00330 (22011) covalent geometry : angle 0.64069 (29697) hydrogen bonds : bond 0.03362 ( 931) hydrogen bonds : angle 4.35130 ( 2601) *********************** 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 298 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8848 (tmm) cc_final: 0.8647 (tmm) REVERT: A 236 LEU cc_start: 0.8921 (pp) cc_final: 0.8663 (pp) REVERT: A 388 ARG cc_start: 0.8963 (mtt180) cc_final: 0.8718 (mtt90) REVERT: A 599 PHE cc_start: 0.8872 (m-80) cc_final: 0.8489 (m-10) REVERT: A 755 LEU cc_start: 0.9085 (pp) cc_final: 0.8719 (tt) REVERT: A 775 MET cc_start: 0.7538 (ppp) cc_final: 0.7257 (ppp) REVERT: A 793 MET cc_start: 0.6617 (mmm) cc_final: 0.6309 (mmm) REVERT: A 808 MET cc_start: 0.8149 (tmm) cc_final: 0.7221 (ttp) REVERT: A 875 MET cc_start: 0.7915 (tmm) cc_final: 0.6704 (mtm) REVERT: A 899 LEU cc_start: 0.9171 (mt) cc_final: 0.8907 (mt) REVERT: A 902 HIS cc_start: 0.8192 (p90) cc_final: 0.7446 (t-90) REVERT: B 158 LEU cc_start: 0.9003 (mt) cc_final: 0.8510 (tp) REVERT: B 175 LYS cc_start: 0.8218 (tptp) cc_final: 0.7742 (mptt) REVERT: B 274 MET cc_start: 0.8371 (mmm) cc_final: 0.8010 (mmm) REVERT: B 321 LEU cc_start: 0.9179 (mt) cc_final: 0.8926 (tt) REVERT: B 562 TYR cc_start: 0.8416 (t80) cc_final: 0.8005 (t80) REVERT: B 659 PHE cc_start: 0.8141 (m-10) cc_final: 0.7890 (m-10) REVERT: B 692 LEU cc_start: 0.9586 (tp) cc_final: 0.9078 (tp) REVERT: B 717 LEU cc_start: 0.9539 (mm) cc_final: 0.8846 (mm) REVERT: B 718 MET cc_start: 0.9106 (ppp) cc_final: 0.8863 (ppp) REVERT: B 770 MET cc_start: 0.6401 (tmm) cc_final: 0.6183 (tmm) REVERT: B 808 MET cc_start: 0.5340 (mtt) cc_final: 0.4114 (mpp) REVERT: B 994 LEU cc_start: 0.8682 (mt) cc_final: 0.8421 (mt) REVERT: C 106 LYS cc_start: 0.9417 (mttt) cc_final: 0.8917 (tttt) REVERT: C 184 MET cc_start: 0.8488 (ttt) cc_final: 0.8240 (tpp) REVERT: C 401 VAL cc_start: 0.9578 (t) cc_final: 0.9362 (t) REVERT: C 487 TYR cc_start: 0.8507 (m-80) cc_final: 0.8045 (m-80) REVERT: C 571 LEU cc_start: 0.9494 (mm) cc_final: 0.9263 (mt) REVERT: C 597 ASP cc_start: 0.9086 (m-30) cc_final: 0.8743 (m-30) REVERT: C 599 PHE cc_start: 0.9174 (m-80) cc_final: 0.8774 (m-80) REVERT: C 765 LEU cc_start: 0.7929 (tp) cc_final: 0.7534 (tp) REVERT: C 775 MET cc_start: 0.8328 (ppp) cc_final: 0.7835 (ppp) REVERT: C 792 LYS cc_start: 0.7599 (mttt) cc_final: 0.7172 (ttpt) REVERT: C 875 MET cc_start: 0.7987 (pmm) cc_final: 0.7648 (pmm) REVERT: C 958 MET cc_start: 0.7609 (mmp) cc_final: 0.7080 (mmm) REVERT: C 970 PHE cc_start: 0.9552 (p90) cc_final: 0.9224 (p90) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1342 time to fit residues: 64.6865 Evaluate side-chains 218 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 266 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 232 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 269 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 HIS A 934 ASN B 162 GLN B 357 HIS ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.082107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.061044 restraints weight = 117772.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.062957 restraints weight = 71978.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.064235 restraints weight = 51360.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.065118 restraints weight = 40604.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.065719 restraints weight = 34410.999| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22011 Z= 0.113 Angle : 0.622 11.889 29697 Z= 0.315 Chirality : 0.040 0.222 3420 Planarity : 0.003 0.050 3765 Dihedral : 4.632 29.925 2871 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.04 % Allowed : 0.83 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.17), residues: 2700 helix: 1.45 (0.16), residues: 1191 sheet: -0.44 (0.28), residues: 339 loop : -1.33 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 691 TYR 0.016 0.001 TYR C 594 PHE 0.023 0.001 PHE C 957 TRP 0.040 0.002 TRP A 888 HIS 0.009 0.001 HIS A 744 Details of bonding type rmsd covalent geometry : bond 0.00240 (22011) covalent geometry : angle 0.62175 (29697) hydrogen bonds : bond 0.03148 ( 931) hydrogen bonds : angle 4.18561 ( 2601) *********************** 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 306 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ARG cc_start: 0.8962 (mtt180) cc_final: 0.8699 (mtt180) REVERT: A 755 LEU cc_start: 0.9076 (pp) cc_final: 0.8723 (tt) REVERT: A 775 MET cc_start: 0.7505 (ppp) cc_final: 0.7221 (ppp) REVERT: A 793 MET cc_start: 0.6789 (mmm) cc_final: 0.6393 (mmm) REVERT: A 808 MET cc_start: 0.7963 (tmm) cc_final: 0.7055 (ttp) REVERT: A 875 MET cc_start: 0.7903 (tmm) cc_final: 0.6789 (mtm) REVERT: A 902 HIS cc_start: 0.8235 (p90) cc_final: 0.7444 (t-90) REVERT: A 1002 LEU cc_start: 0.8918 (tp) cc_final: 0.8635 (tp) REVERT: B 158 LEU cc_start: 0.8914 (mt) cc_final: 0.8471 (tp) REVERT: B 175 LYS cc_start: 0.8123 (tptp) cc_final: 0.7813 (mptt) REVERT: B 274 MET cc_start: 0.8377 (mmm) cc_final: 0.8075 (mmm) REVERT: B 321 LEU cc_start: 0.9143 (mt) cc_final: 0.8899 (tt) REVERT: B 562 TYR cc_start: 0.8376 (t80) cc_final: 0.7940 (t80) REVERT: B 659 PHE cc_start: 0.8185 (m-10) cc_final: 0.7725 (m-10) REVERT: B 770 MET cc_start: 0.6392 (tmm) cc_final: 0.6184 (tmm) REVERT: B 808 MET cc_start: 0.5405 (mtt) cc_final: 0.4127 (mpp) REVERT: B 994 LEU cc_start: 0.8643 (mt) cc_final: 0.8408 (mt) REVERT: B 1002 LEU cc_start: 0.9095 (tp) cc_final: 0.8153 (tp) REVERT: B 1005 TRP cc_start: 0.7833 (m100) cc_final: 0.7344 (m100) REVERT: C 106 LYS cc_start: 0.9424 (mttt) cc_final: 0.8936 (tttt) REVERT: C 184 MET cc_start: 0.8462 (ttt) cc_final: 0.8215 (tpp) REVERT: C 317 LEU cc_start: 0.9195 (mt) cc_final: 0.8950 (mt) REVERT: C 401 VAL cc_start: 0.9517 (t) cc_final: 0.9273 (t) REVERT: C 487 TYR cc_start: 0.8481 (m-80) cc_final: 0.8070 (m-80) REVERT: C 550 ASN cc_start: 0.8957 (m-40) cc_final: 0.8539 (m-40) REVERT: C 571 LEU cc_start: 0.9475 (mm) cc_final: 0.9229 (mt) REVERT: C 597 ASP cc_start: 0.9091 (m-30) cc_final: 0.8786 (m-30) REVERT: C 599 PHE cc_start: 0.9164 (m-80) cc_final: 0.8777 (m-80) REVERT: C 765 LEU cc_start: 0.8011 (tp) cc_final: 0.7653 (tp) REVERT: C 775 MET cc_start: 0.8353 (ppp) cc_final: 0.7716 (ppp) REVERT: C 792 LYS cc_start: 0.7474 (mttt) cc_final: 0.7049 (ttpt) REVERT: C 793 MET cc_start: 0.6619 (mmm) cc_final: 0.6389 (mmm) REVERT: C 958 MET cc_start: 0.7617 (mmp) cc_final: 0.7031 (mmm) REVERT: C 970 PHE cc_start: 0.9537 (p90) cc_final: 0.9229 (p90) outliers start: 1 outliers final: 0 residues processed: 306 average time/residue: 0.1275 time to fit residues: 63.3191 Evaluate side-chains 225 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 10.0000 chunk 217 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 32 optimal weight: 0.0170 chunk 117 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 HIS A 934 ASN B 162 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS ** C 858 ASN ** 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 = 0.3736 r_free = 0.3736 target = 0.082285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.061059 restraints weight = 115263.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.063021 restraints weight = 69778.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.064331 restraints weight = 49403.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.065235 restraints weight = 38789.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.065843 restraints weight = 32695.208| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22011 Z= 0.104 Angle : 0.619 11.512 29697 Z= 0.311 Chirality : 0.041 0.205 3420 Planarity : 0.003 0.058 3765 Dihedral : 4.551 28.991 2871 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2700 helix: 1.49 (0.16), residues: 1191 sheet: -0.37 (0.29), residues: 327 loop : -1.36 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 691 TYR 0.020 0.001 TYR C 594 PHE 0.023 0.001 PHE C 957 TRP 0.029 0.002 TRP A 888 HIS 0.010 0.001 HIS C 744 Details of bonding type rmsd covalent geometry : bond 0.00221 (22011) covalent geometry : angle 0.61882 (29697) hydrogen bonds : bond 0.02998 ( 931) hydrogen bonds : angle 4.10446 ( 2601) *********************** 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 304 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.867 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 388 ARG cc_start: 0.8976 (mtt180) cc_final: 0.8707 (mtt180) REVERT: A 755 LEU cc_start: 0.9165 (pp) cc_final: 0.8822 (tt) REVERT: A 775 MET cc_start: 0.7442 (ppp) cc_final: 0.7159 (ppp) REVERT: A 793 MET cc_start: 0.6518 (mmm) cc_final: 0.6223 (mmm) REVERT: A 875 MET cc_start: 0.7787 (tmm) cc_final: 0.6605 (mtm) REVERT: A 902 HIS cc_start: 0.8262 (p90) cc_final: 0.7488 (t-90) REVERT: A 1002 LEU cc_start: 0.8845 (tp) cc_final: 0.8561 (tp) REVERT: B 175 LYS cc_start: 0.8070 (tptp) cc_final: 0.7806 (mptt) REVERT: B 274 MET cc_start: 0.8305 (mmm) cc_final: 0.8048 (mmm) REVERT: B 321 LEU cc_start: 0.9149 (mt) cc_final: 0.8906 (tt) REVERT: B 659 PHE cc_start: 0.8145 (m-10) cc_final: 0.7892 (m-10) REVERT: B 770 MET cc_start: 0.6379 (tmm) cc_final: 0.6067 (tmm) REVERT: B 808 MET cc_start: 0.5406 (mtt) cc_final: 0.4162 (mpp) REVERT: B 994 LEU cc_start: 0.8580 (mt) cc_final: 0.8357 (mt) REVERT: B 1002 LEU cc_start: 0.9044 (tp) cc_final: 0.8128 (tp) REVERT: B 1005 TRP cc_start: 0.7806 (m100) cc_final: 0.7465 (m100) REVERT: C 106 LYS cc_start: 0.9446 (mttt) cc_final: 0.8964 (tttm) REVERT: C 184 MET cc_start: 0.8467 (ttt) cc_final: 0.8214 (tpp) REVERT: C 213 PHE cc_start: 0.7385 (t80) cc_final: 0.7139 (t80) REVERT: C 401 VAL cc_start: 0.9511 (t) cc_final: 0.9262 (t) REVERT: C 487 TYR cc_start: 0.8414 (m-80) cc_final: 0.7935 (m-80) REVERT: C 550 ASN cc_start: 0.8956 (m-40) cc_final: 0.8521 (m-40) REVERT: C 571 LEU cc_start: 0.9479 (mm) cc_final: 0.9194 (mt) REVERT: C 597 ASP cc_start: 0.9030 (m-30) cc_final: 0.8744 (m-30) REVERT: C 599 PHE cc_start: 0.9106 (m-80) cc_final: 0.8794 (m-80) REVERT: C 775 MET cc_start: 0.8473 (ppp) cc_final: 0.7840 (ppp) REVERT: C 958 MET cc_start: 0.7688 (mmp) cc_final: 0.7071 (mmm) REVERT: C 970 PHE cc_start: 0.9537 (p90) cc_final: 0.9264 (p90) outliers start: 1 outliers final: 0 residues processed: 304 average time/residue: 0.1261 time to fit residues: 63.1442 Evaluate side-chains 233 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 7 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 209 optimal weight: 0.9990 chunk 238 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 28 optimal weight: 0.1980 chunk 81 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 HIS A 934 ASN B 162 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.080620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.059289 restraints weight = 116879.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.061184 restraints weight = 71149.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.062441 restraints weight = 50848.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.063305 restraints weight = 40350.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.063886 restraints weight = 34329.538| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.6356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22011 Z= 0.142 Angle : 0.650 12.320 29697 Z= 0.331 Chirality : 0.041 0.206 3420 Planarity : 0.004 0.049 3765 Dihedral : 4.771 28.199 2871 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.04 % Allowed : 0.29 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.17), residues: 2700 helix: 1.50 (0.16), residues: 1170 sheet: -0.28 (0.29), residues: 312 loop : -1.40 (0.19), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 691 TYR 0.015 0.001 TYR B 487 PHE 0.026 0.002 PHE B 579 TRP 0.029 0.002 TRP A 888 HIS 0.010 0.001 HIS A 744 Details of bonding type rmsd covalent geometry : bond 0.00306 (22011) covalent geometry : angle 0.65019 (29697) hydrogen bonds : bond 0.03314 ( 931) hydrogen bonds : angle 4.31939 ( 2601) ********************** 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 280 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 0.846 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 236 LEU cc_start: 0.9107 (pp) cc_final: 0.8825 (pp) REVERT: A 388 ARG cc_start: 0.8982 (mtt180) cc_final: 0.8734 (mtt180) REVERT: A 718 MET cc_start: 0.8138 (ppp) cc_final: 0.7905 (ppp) REVERT: A 755 LEU cc_start: 0.9132 (pp) cc_final: 0.8815 (tt) REVERT: A 793 MET cc_start: 0.6421 (mmm) cc_final: 0.6101 (mmm) REVERT: A 875 MET cc_start: 0.7870 (tmm) cc_final: 0.6743 (mtm) REVERT: A 902 HIS cc_start: 0.8224 (p90) cc_final: 0.7449 (t-90) REVERT: A 1010 ASP cc_start: 0.8518 (m-30) cc_final: 0.7997 (p0) REVERT: B 175 LYS cc_start: 0.8074 (tptp) cc_final: 0.7776 (mptt) REVERT: B 274 MET cc_start: 0.8387 (mmm) cc_final: 0.8108 (mmm) REVERT: B 321 LEU cc_start: 0.9180 (mt) cc_final: 0.8955 (tt) REVERT: B 562 TYR cc_start: 0.8574 (t80) cc_final: 0.8195 (t80) REVERT: B 659 PHE cc_start: 0.8173 (m-10) cc_final: 0.7889 (m-10) REVERT: B 714 ILE cc_start: 0.8467 (mt) cc_final: 0.7830 (tp) REVERT: B 770 MET cc_start: 0.6445 (tmm) cc_final: 0.6155 (tmm) REVERT: B 808 MET cc_start: 0.5655 (mtt) cc_final: 0.4340 (mpp) REVERT: B 1002 LEU cc_start: 0.9027 (tp) cc_final: 0.7903 (tp) REVERT: B 1005 TRP cc_start: 0.7972 (m100) cc_final: 0.7486 (m100) REVERT: C 106 LYS cc_start: 0.9490 (mttt) cc_final: 0.9017 (mmmt) REVERT: C 184 MET cc_start: 0.8541 (ttt) cc_final: 0.8246 (tpp) REVERT: C 213 PHE cc_start: 0.7677 (t80) cc_final: 0.7287 (t80) REVERT: C 317 LEU cc_start: 0.9202 (mt) cc_final: 0.8973 (mt) REVERT: C 401 VAL cc_start: 0.9564 (t) cc_final: 0.9321 (t) REVERT: C 487 TYR cc_start: 0.8607 (m-80) cc_final: 0.8037 (m-80) REVERT: C 550 ASN cc_start: 0.8973 (m-40) cc_final: 0.8528 (m-40) REVERT: C 571 LEU cc_start: 0.9503 (mm) cc_final: 0.9256 (mt) REVERT: C 597 ASP cc_start: 0.9042 (m-30) cc_final: 0.8780 (m-30) REVERT: C 599 PHE cc_start: 0.9151 (m-80) cc_final: 0.8671 (m-80) REVERT: C 692 LEU cc_start: 0.9480 (tt) cc_final: 0.9280 (tt) REVERT: C 775 MET cc_start: 0.8492 (ppp) cc_final: 0.7793 (ppp) REVERT: C 875 MET cc_start: 0.7851 (pmm) cc_final: 0.7412 (pmm) REVERT: C 958 MET cc_start: 0.7365 (mmp) cc_final: 0.6727 (mmm) REVERT: C 970 PHE cc_start: 0.9525 (p90) cc_final: 0.9266 (p90) REVERT: C 999 GLU cc_start: 0.8041 (tp30) cc_final: 0.7655 (tm-30) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.1245 time to fit residues: 57.5849 Evaluate side-chains 215 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 127 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 241 optimal weight: 0.0770 chunk 109 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 235 optimal weight: 0.0770 chunk 144 optimal weight: 7.9990 chunk 201 optimal weight: 0.7980 chunk 190 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 ASN B 162 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.082559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.061441 restraints weight = 116017.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.063392 restraints weight = 70136.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.064730 restraints weight = 49614.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.065630 restraints weight = 38914.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.066236 restraints weight = 32848.940| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22011 Z= 0.102 Angle : 0.619 11.532 29697 Z= 0.310 Chirality : 0.040 0.193 3420 Planarity : 0.003 0.045 3765 Dihedral : 4.572 27.444 2871 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.04 % Allowed : 0.08 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2700 helix: 1.70 (0.16), residues: 1155 sheet: -0.21 (0.30), residues: 312 loop : -1.43 (0.19), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 530 TYR 0.011 0.001 TYR A 449 PHE 0.023 0.001 PHE C 957 TRP 0.023 0.002 TRP A 888 HIS 0.007 0.001 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00211 (22011) covalent geometry : angle 0.61925 (29697) hydrogen bonds : bond 0.02879 ( 931) hydrogen bonds : angle 4.11355 ( 2601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3903.83 seconds wall clock time: 68 minutes 22.11 seconds (4102.11 seconds total)