Starting phenix.real_space_refine on Wed Jun 18 23:26:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fw9_29498/06_2025/8fw9_29498_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fw9_29498/06_2025/8fw9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fw9_29498/06_2025/8fw9_29498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fw9_29498/06_2025/8fw9_29498.map" model { file = "/net/cci-nas-00/data/ceres_data/8fw9_29498/06_2025/8fw9_29498_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fw9_29498/06_2025/8fw9_29498_neut.cif" } resolution = 4.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21612 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7204 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Chain: "B" Number of atoms: 7204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7204 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Chain: "C" Number of atoms: 7204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7204 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Time building chain proxies: 13.94, per 1000 atoms: 0.65 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: 5.04 Conformation dependent library (CDL) restraints added in 2.6 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: 2.79 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: 8.50 Time building geometry restraints manager: 6.04 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 50.670 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.100 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (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 TRP 0.034 0.007 TRP A 917 HIS 0.004 0.001 HIS A 797 PHE 0.020 0.003 PHE C 957 TYR 0.031 0.004 TYR B 449 ARG 0.002 0.000 ARG C 526 Details of bonding type rmsd hydrogen bonds : bond 0.17694 ( 931) hydrogen bonds : angle 6.99691 ( 2601) covalent geometry : bond 0.01173 (22011) covalent geometry : angle 1.19483 (29697) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 648 time to evaluate : 2.514 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: 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: 0.9092 (mmt) cc_final: 0.8280 (mmm) REVERT: A 353 GLU cc_start: 0.8055 (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: 0.7320 (p90) REVERT: A 584 LEU cc_start: 0.9252 (tp) cc_final: 0.9041 (tt) REVERT: A 659 PHE cc_start: 0.8894 (m-80) cc_final: 0.8435 (m-10) REVERT: A 716 SER cc_start: 0.9137 (t) cc_final: 0.8439 (m) REVERT: A 740 THR cc_start: 0.8431 (m) cc_final: 0.8231 (p) REVERT: A 793 MET cc_start: 0.6809 (mmm) cc_final: 0.6587 (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: 0.7661 (mm-40) REVERT: B 197 PHE cc_start: 0.8763 (m-80) cc_final: 0.8466 (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: 0.6964 (mmp) cc_final: 0.6653 (mmp) REVERT: B 954 TRP cc_start: 0.7003 (m-90) cc_final: 0.6452 (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: 0.8650 (tp) REVERT: C 244 LEU cc_start: 0.9244 (mt) cc_final: 0.8853 (mp) REVERT: C 444 LYS cc_start: 0.9191 (mttt) cc_final: 0.8953 (tttm) REVERT: C 571 LEU cc_start: 0.9482 (mt) cc_final: 0.9275 (mm) REVERT: C 585 TYR cc_start: 0.8885 (t80) cc_final: 0.8113 (t80) REVERT: C 615 ASP cc_start: 0.8211 (t0) cc_final: 0.7773 (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: 0.7437 (tp40) REVERT: C 944 LEU cc_start: 0.8227 (tt) cc_final: 0.8027 (tt) outliers start: 2 outliers final: 1 residues processed: 650 average time/residue: 0.3917 time to fit residues: 382.7531 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 : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 0.7980 chunk 204 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 138 optimal weight: 0.0010 chunk 109 optimal weight: 0.8980 chunk 211 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 157 optimal weight: 0.1980 chunk 245 optimal weight: 8.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.085454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.064307 restraints weight = 113238.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.066448 restraints weight = 66344.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.067919 restraints weight = 45637.860| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3273 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= 0.146 Angle : 0.647 12.028 29697 Z= 0.343 Chirality : 0.040 0.210 3420 Planarity : 0.004 0.057 3765 Dihedral : 4.859 40.371 2871 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.81 % Favored : 94.11 % Rotamer: Outliers : 0.17 % Allowed : 1.98 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 4.55 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2700 helix: 1.14 (0.15), residues: 1179 sheet: 0.07 (0.28), residues: 312 loop : -1.10 (0.19), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 186 HIS 0.004 0.001 HIS A 744 PHE 0.024 0.002 PHE A 957 TYR 0.014 0.001 TYR A 473 ARG 0.010 0.001 ARG C 691 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 931) hydrogen bonds : angle 5.00905 ( 2601) covalent geometry : bond 0.00302 (22011) covalent geometry : angle 0.64690 (29697) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 450 time to evaluate : 2.462 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: A 184 MET cc_start: 0.8795 (tmm) cc_final: 0.8545 (tmm) REVERT: A 233 MET cc_start: 0.8871 (mmt) cc_final: 0.8128 (mmm) REVERT: A 309 ILE cc_start: 0.9527 (mt) cc_final: 0.9264 (tp) REVERT: A 321 LEU cc_start: 0.9085 (tp) cc_final: 0.8880 (tt) REVERT: A 408 PHE cc_start: 0.8685 (m-80) cc_final: 0.8307 (m-10) REVERT: A 503 ARG cc_start: 0.9106 (mtp85) cc_final: 0.8905 (mtp85) REVERT: A 513 TYR cc_start: 0.7118 (p90) cc_final: 0.6868 (p90) REVERT: A 571 LEU cc_start: 0.9337 (mm) cc_final: 0.9128 (mm) REVERT: A 599 PHE cc_start: 0.8716 (m-80) cc_final: 0.7628 (m-10) REVERT: A 755 LEU cc_start: 0.9172 (pp) cc_final: 0.8804 (tt) REVERT: A 793 MET cc_start: 0.6662 (mmm) cc_final: 0.6103 (mmm) REVERT: B 114 PHE cc_start: 0.8225 (t80) cc_final: 0.8004 (t80) REVERT: B 185 LEU cc_start: 0.9574 (mt) cc_final: 0.9018 (mt) REVERT: B 480 ILE cc_start: 0.9087 (mm) cc_final: 0.8683 (tt) REVERT: B 584 LEU cc_start: 0.9307 (tp) cc_final: 0.9052 (tp) REVERT: B 659 PHE cc_start: 0.7426 (m-10) cc_final: 0.6547 (t80) REVERT: B 680 LEU cc_start: 0.9296 (mt) cc_final: 0.9061 (mt) REVERT: B 694 ILE cc_start: 0.9477 (mp) cc_final: 0.9242 (tt) REVERT: B 732 ILE cc_start: 0.8807 (mt) cc_final: 0.8569 (pt) REVERT: B 770 MET cc_start: 0.7036 (tmm) cc_final: 0.6571 (tmm) REVERT: B 795 LEU cc_start: 0.8861 (mt) cc_final: 0.8649 (mm) REVERT: B 796 PHE cc_start: 0.8818 (t80) cc_final: 0.8564 (t80) REVERT: B 808 MET cc_start: 0.5893 (mtt) cc_final: 0.4486 (mpp) REVERT: B 1002 LEU cc_start: 0.8904 (tp) cc_final: 0.7912 (tp) REVERT: B 1005 TRP cc_start: 0.8201 (m100) cc_final: 0.7602 (m100) REVERT: C 106 LYS cc_start: 0.9203 (mttt) cc_final: 0.8673 (mmmt) REVERT: C 122 GLU cc_start: 0.8168 (mp0) cc_final: 0.7909 (tp30) REVERT: C 215 THR cc_start: 0.9280 (m) cc_final: 0.9001 (p) REVERT: C 248 ASP cc_start: 0.8410 (t0) cc_final: 0.8042 (t0) REVERT: C 337 THR cc_start: 0.9140 (m) cc_final: 0.8849 (p) REVERT: C 401 VAL cc_start: 0.9417 (t) cc_final: 0.9107 (t) REVERT: C 411 GLN cc_start: 0.8987 (pm20) cc_final: 0.8737 (pm20) REVERT: C 487 TYR cc_start: 0.8411 (m-80) cc_final: 0.7822 (m-80) REVERT: C 792 LYS cc_start: 0.7345 (mttt) cc_final: 0.6997 (ttpt) REVERT: C 998 GLN cc_start: 0.9198 (pm20) cc_final: 0.8984 (pm20) outliers start: 4 outliers final: 0 residues processed: 453 average time/residue: 0.3258 time to fit residues: 231.4175 Evaluate side-chains 289 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 10.0000 chunk 233 optimal weight: 0.0970 chunk 265 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 258 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 286 HIS A 348 GLN A 357 HIS A 374 ASN A 675 GLN A 744 HIS B 103 GLN B 155 ASN B 162 GLN B 865 ASN ** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3735 r_free = 0.3735 target = 0.082508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.061346 restraints weight = 114747.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.063324 restraints weight = 68500.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.064677 restraints weight = 48279.427| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22011 Z= 0.147 Angle : 0.640 12.817 29697 Z= 0.334 Chirality : 0.040 0.194 3420 Planarity : 0.004 0.055 3765 Dihedral : 4.887 33.927 2871 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.03 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.17), residues: 2700 helix: 1.39 (0.16), residues: 1146 sheet: -0.28 (0.28), residues: 324 loop : -1.13 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 917 HIS 0.007 0.001 HIS A 744 PHE 0.026 0.002 PHE B 957 TYR 0.019 0.001 TYR C 250 ARG 0.007 0.001 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 931) hydrogen bonds : angle 4.71166 ( 2601) covalent geometry : bond 0.00312 (22011) covalent geometry : angle 0.63978 (29697) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 2.515 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: A 95 GLU cc_start: 0.7949 (pp20) cc_final: 0.7711 (pm20) REVERT: A 197 PHE cc_start: 0.8583 (m-80) cc_final: 0.8247 (m-80) REVERT: A 321 LEU cc_start: 0.9165 (tp) cc_final: 0.8827 (tt) REVERT: A 503 ARG cc_start: 0.9122 (mtp85) cc_final: 0.8833 (mtp85) REVERT: A 513 TYR cc_start: 0.7143 (p90) cc_final: 0.6920 (p90) REVERT: A 571 LEU cc_start: 0.9327 (mm) cc_final: 0.8903 (mm) REVERT: A 755 LEU cc_start: 0.9152 (pp) cc_final: 0.8854 (tt) REVERT: A 793 MET cc_start: 0.6478 (mmm) cc_final: 0.6189 (mmm) REVERT: A 902 HIS cc_start: 0.8377 (p90) cc_final: 0.7962 (p-80) REVERT: B 158 LEU cc_start: 0.8970 (mt) cc_final: 0.8478 (tp) REVERT: B 185 LEU cc_start: 0.9656 (mt) cc_final: 0.9386 (mt) REVERT: B 274 MET cc_start: 0.8335 (mmm) cc_final: 0.7683 (mmm) REVERT: B 477 MET cc_start: 0.6233 (mmm) cc_final: 0.5978 (mmm) REVERT: B 562 TYR cc_start: 0.8202 (t80) cc_final: 0.7804 (t80) REVERT: B 584 LEU cc_start: 0.9331 (tp) cc_final: 0.9114 (tp) REVERT: B 612 ILE cc_start: 0.7739 (mm) cc_final: 0.7461 (mm) REVERT: B 680 LEU cc_start: 0.9303 (mt) cc_final: 0.9036 (mt) REVERT: B 732 ILE cc_start: 0.8899 (mt) cc_final: 0.8680 (pt) REVERT: B 808 MET cc_start: 0.5468 (mtt) cc_final: 0.4089 (mpp) REVERT: B 969 PHE cc_start: 0.8741 (p90) cc_final: 0.8509 (p90) REVERT: C 106 LYS cc_start: 0.9396 (mttt) cc_final: 0.8959 (mmmt) REVERT: C 122 GLU cc_start: 0.8286 (mp0) cc_final: 0.7862 (tp30) REVERT: C 184 MET cc_start: 0.8712 (ttm) cc_final: 0.8388 (tpp) REVERT: C 321 LEU cc_start: 0.9130 (tp) cc_final: 0.8929 (tt) REVERT: C 337 THR cc_start: 0.9114 (m) cc_final: 0.8827 (p) REVERT: C 401 VAL cc_start: 0.9531 (t) cc_final: 0.9292 (t) REVERT: C 487 TYR cc_start: 0.8454 (m-80) cc_final: 0.8069 (m-80) REVERT: C 571 LEU cc_start: 0.9589 (mm) cc_final: 0.9297 (mt) REVERT: C 585 TYR cc_start: 0.7710 (t80) cc_final: 0.7399 (t80) REVERT: C 597 ASP cc_start: 0.9176 (m-30) cc_final: 0.8902 (m-30) REVERT: C 765 LEU cc_start: 0.7955 (tp) cc_final: 0.7579 (tp) REVERT: C 792 LYS cc_start: 0.7471 (mttt) cc_final: 0.7062 (ttpp) REVERT: C 958 MET cc_start: 0.8397 (mmp) cc_final: 0.7958 (mmm) REVERT: C 970 PHE cc_start: 0.9380 (p90) cc_final: 0.9109 (p90) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.3121 time to fit residues: 175.6174 Evaluate side-chains 253 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 62 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 266 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 chunk 150 optimal weight: 0.0570 chunk 149 optimal weight: 0.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- 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 B 162 GLN B 772 ASN C 145 HIS C 147 HIS ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 ASN C 604 ASN ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.080929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.059785 restraints weight = 117493.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.061727 restraints weight = 70404.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.063048 restraints weight = 49749.999| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22011 Z= 0.155 Angle : 0.631 12.278 29697 Z= 0.328 Chirality : 0.040 0.199 3420 Planarity : 0.004 0.056 3765 Dihedral : 4.949 34.080 2871 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.03 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2700 helix: 1.17 (0.16), residues: 1188 sheet: 0.00 (0.28), residues: 306 loop : -1.52 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 954 HIS 0.016 0.001 HIS A 744 PHE 0.019 0.002 PHE B 957 TYR 0.017 0.002 TYR C 594 ARG 0.008 0.001 ARG C 207 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 931) hydrogen bonds : angle 4.62607 ( 2601) covalent geometry : bond 0.00333 (22011) covalent geometry : angle 0.63096 (29697) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 2.425 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 95 GLU cc_start: 0.8110 (pp20) cc_final: 0.7811 (pm20) REVERT: A 321 LEU cc_start: 0.9152 (tp) cc_final: 0.8918 (tt) REVERT: A 388 ARG cc_start: 0.9125 (mtt180) cc_final: 0.8885 (mtt90) REVERT: A 503 ARG cc_start: 0.9269 (mtp85) cc_final: 0.8885 (mtp85) REVERT: A 611 PHE cc_start: 0.7953 (m-80) cc_final: 0.7697 (m-10) REVERT: A 755 LEU cc_start: 0.9165 (pp) cc_final: 0.8842 (tt) REVERT: A 770 MET cc_start: 0.7962 (mmm) cc_final: 0.7630 (mmp) REVERT: A 793 MET cc_start: 0.6528 (mmm) cc_final: 0.6156 (mmm) REVERT: A 875 MET cc_start: 0.7992 (tmm) cc_final: 0.6623 (mtm) REVERT: A 899 LEU cc_start: 0.9279 (mt) cc_final: 0.9031 (mt) REVERT: A 902 HIS cc_start: 0.8344 (p90) cc_final: 0.7360 (t-90) REVERT: A 994 LEU cc_start: 0.8752 (tp) cc_final: 0.8430 (tp) REVERT: B 158 LEU cc_start: 0.9036 (mt) cc_final: 0.8500 (tp) REVERT: B 197 PHE cc_start: 0.7735 (m-10) cc_final: 0.7444 (m-10) REVERT: B 274 MET cc_start: 0.8279 (mmm) cc_final: 0.7766 (mmm) REVERT: B 562 TYR cc_start: 0.8417 (t80) cc_final: 0.8009 (t80) REVERT: B 612 ILE cc_start: 0.7779 (mm) cc_final: 0.7553 (mm) REVERT: B 717 LEU cc_start: 0.9518 (mm) cc_final: 0.9281 (tp) REVERT: B 732 ILE cc_start: 0.8921 (mt) cc_final: 0.8697 (pt) REVERT: B 770 MET cc_start: 0.6521 (tmm) cc_final: 0.6022 (tmm) REVERT: B 994 LEU cc_start: 0.8600 (mt) cc_final: 0.8392 (mt) REVERT: C 106 LYS cc_start: 0.9411 (mttt) cc_final: 0.8920 (tttt) REVERT: C 122 GLU cc_start: 0.8203 (mp0) cc_final: 0.7818 (tp30) REVERT: C 184 MET cc_start: 0.8714 (ttm) cc_final: 0.8356 (tpp) REVERT: C 321 LEU cc_start: 0.9142 (tp) cc_final: 0.8898 (tt) REVERT: C 337 THR cc_start: 0.9107 (m) cc_final: 0.8816 (p) REVERT: C 401 VAL cc_start: 0.9548 (t) cc_final: 0.9314 (t) REVERT: C 487 TYR cc_start: 0.8551 (m-80) cc_final: 0.8076 (m-80) REVERT: C 550 ASN cc_start: 0.8981 (m110) cc_final: 0.8608 (m-40) REVERT: C 571 LEU cc_start: 0.9584 (mm) cc_final: 0.9354 (mt) REVERT: C 576 GLU cc_start: 0.9456 (tt0) cc_final: 0.9244 (tt0) REVERT: C 597 ASP cc_start: 0.9155 (m-30) cc_final: 0.8902 (m-30) REVERT: C 599 PHE cc_start: 0.9252 (m-80) cc_final: 0.8832 (m-80) REVERT: C 659 PHE cc_start: 0.8137 (m-10) cc_final: 0.7906 (m-10) REVERT: C 765 LEU cc_start: 0.8035 (tp) cc_final: 0.7649 (tp) REVERT: C 792 LYS cc_start: 0.7705 (mttt) cc_final: 0.7250 (ttpt) REVERT: C 875 MET cc_start: 0.8289 (pmm) cc_final: 0.8005 (pmm) REVERT: C 958 MET cc_start: 0.8169 (mmp) cc_final: 0.7881 (mmm) REVERT: C 970 PHE cc_start: 0.9494 (p90) cc_final: 0.9192 (p90) REVERT: C 999 GLU cc_start: 0.7854 (tp30) cc_final: 0.7357 (tp30) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.3129 time to fit residues: 153.8044 Evaluate side-chains 239 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 26 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 249 optimal weight: 0.0970 chunk 60 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 195 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 168 optimal weight: 20.0000 chunk 219 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** B 162 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS C 147 HIS ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.081409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.060531 restraints weight = 117253.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.062372 restraints weight = 71879.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.063643 restraints weight = 51622.644| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22011 Z= 0.131 Angle : 0.608 12.103 29697 Z= 0.314 Chirality : 0.040 0.189 3420 Planarity : 0.004 0.051 3765 Dihedral : 4.865 32.703 2871 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % 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 : 3.03 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2700 helix: 1.21 (0.16), residues: 1203 sheet: -0.01 (0.28), residues: 306 loop : -1.65 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 954 HIS 0.007 0.001 HIS A 601 PHE 0.019 0.002 PHE C 957 TYR 0.022 0.001 TYR A 715 ARG 0.006 0.000 ARG C 691 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 931) hydrogen bonds : angle 4.47183 ( 2601) covalent geometry : bond 0.00280 (22011) covalent geometry : angle 0.60781 (29697) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 2.539 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: A 95 GLU cc_start: 0.8143 (pp20) cc_final: 0.7900 (pm20) REVERT: A 236 LEU cc_start: 0.9057 (pp) cc_final: 0.8806 (pp) REVERT: A 321 LEU cc_start: 0.9190 (tp) cc_final: 0.8913 (tt) REVERT: A 388 ARG cc_start: 0.9109 (mtt180) cc_final: 0.8709 (mtt-85) REVERT: A 503 ARG cc_start: 0.9241 (mtp85) cc_final: 0.8732 (mtp85) REVERT: A 611 PHE cc_start: 0.7889 (m-80) cc_final: 0.7637 (m-10) REVERT: A 755 LEU cc_start: 0.9221 (pp) cc_final: 0.8899 (tt) REVERT: A 770 MET cc_start: 0.8137 (mmm) cc_final: 0.7848 (mmp) REVERT: A 793 MET cc_start: 0.6622 (mmm) cc_final: 0.6202 (mmm) REVERT: A 831 CYS cc_start: 0.8383 (m) cc_final: 0.7646 (m) REVERT: A 902 HIS cc_start: 0.8362 (p90) cc_final: 0.7966 (p-80) REVERT: A 994 LEU cc_start: 0.8813 (tp) cc_final: 0.8487 (tp) REVERT: A 1010 ASP cc_start: 0.8388 (m-30) cc_final: 0.7777 (p0) REVERT: B 158 LEU cc_start: 0.8984 (mt) cc_final: 0.8504 (tp) REVERT: B 197 PHE cc_start: 0.7798 (m-10) cc_final: 0.7383 (m-80) REVERT: B 274 MET cc_start: 0.8280 (mmm) cc_final: 0.7787 (mmm) REVERT: B 562 TYR cc_start: 0.8388 (t80) cc_final: 0.7962 (t80) REVERT: B 612 ILE cc_start: 0.7787 (mm) cc_final: 0.7569 (mm) REVERT: B 714 ILE cc_start: 0.8753 (pt) cc_final: 0.8514 (tp) REVERT: B 717 LEU cc_start: 0.9550 (mm) cc_final: 0.9192 (mm) REVERT: B 770 MET cc_start: 0.6647 (tmm) cc_final: 0.6232 (tmm) REVERT: B 808 MET cc_start: 0.6847 (mtm) cc_final: 0.5926 (mpp) REVERT: B 970 PHE cc_start: 0.7383 (p90) cc_final: 0.6173 (p90) REVERT: B 972 PHE cc_start: 0.8731 (m-80) cc_final: 0.8445 (m-80) REVERT: B 1002 LEU cc_start: 0.9191 (tp) cc_final: 0.8374 (tp) REVERT: C 106 LYS cc_start: 0.9418 (mttt) cc_final: 0.8923 (tttt) REVERT: C 184 MET cc_start: 0.8635 (ttm) cc_final: 0.8262 (tpp) REVERT: C 213 PHE cc_start: 0.7672 (t80) cc_final: 0.7305 (t80) REVERT: C 321 LEU cc_start: 0.9096 (tp) cc_final: 0.8784 (tt) REVERT: C 401 VAL cc_start: 0.9544 (t) cc_final: 0.9306 (t) REVERT: C 487 TYR cc_start: 0.8521 (m-80) cc_final: 0.8035 (m-80) REVERT: C 550 ASN cc_start: 0.8954 (m-40) cc_final: 0.8461 (m-40) REVERT: C 576 GLU cc_start: 0.9395 (tt0) cc_final: 0.9093 (tt0) REVERT: C 597 ASP cc_start: 0.9100 (m-30) cc_final: 0.8842 (m-30) REVERT: C 599 PHE cc_start: 0.9232 (m-80) cc_final: 0.8760 (m-80) REVERT: C 765 LEU cc_start: 0.8118 (tp) cc_final: 0.7836 (tt) REVERT: C 792 LYS cc_start: 0.7700 (mttt) cc_final: 0.7265 (ttpp) REVERT: C 970 PHE cc_start: 0.9498 (p90) cc_final: 0.9235 (p90) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.3208 time to fit residues: 157.0878 Evaluate side-chains 230 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 265 optimal weight: 10.0000 chunk 246 optimal weight: 6.9990 chunk 249 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 210 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 223 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 B 162 GLN B 357 HIS ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS C 357 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.080774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.059938 restraints weight = 117682.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.061753 restraints weight = 72766.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.062994 restraints weight = 52541.225| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.5776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22011 Z= 0.133 Angle : 0.613 12.581 29697 Z= 0.315 Chirality : 0.040 0.189 3420 Planarity : 0.004 0.049 3765 Dihedral : 4.821 32.164 2871 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2700 helix: 1.26 (0.16), residues: 1218 sheet: -0.03 (0.29), residues: 303 loop : -1.71 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B1005 HIS 0.009 0.001 HIS A 744 PHE 0.031 0.002 PHE A 972 TYR 0.016 0.001 TYR A 715 ARG 0.005 0.000 ARG C 691 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 931) hydrogen bonds : angle 4.35627 ( 2601) covalent geometry : bond 0.00279 (22011) covalent geometry : angle 0.61310 (29697) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 2.472 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 95 GLU cc_start: 0.8195 (pp20) cc_final: 0.7989 (pm20) REVERT: A 228 ARG cc_start: 0.7552 (ttp-170) cc_final: 0.6014 (ttt-90) REVERT: A 236 LEU cc_start: 0.9077 (pp) cc_final: 0.8842 (pp) REVERT: A 321 LEU cc_start: 0.9219 (tp) cc_final: 0.8910 (tt) REVERT: A 388 ARG cc_start: 0.9144 (mtt180) cc_final: 0.8740 (mtt-85) REVERT: A 503 ARG cc_start: 0.9256 (mtp85) cc_final: 0.9036 (ttm110) REVERT: A 611 PHE cc_start: 0.7999 (m-80) cc_final: 0.7617 (m-10) REVERT: A 755 LEU cc_start: 0.9166 (pp) cc_final: 0.8838 (tt) REVERT: A 770 MET cc_start: 0.8017 (mmm) cc_final: 0.7671 (mmp) REVERT: A 793 MET cc_start: 0.6590 (mmm) cc_final: 0.6125 (mmm) REVERT: A 808 MET cc_start: 0.8097 (tmm) cc_final: 0.7128 (ttp) REVERT: A 826 GLN cc_start: 0.8989 (mp10) cc_final: 0.8510 (mp10) REVERT: A 875 MET cc_start: 0.8022 (tmm) cc_final: 0.6890 (mtm) REVERT: A 899 LEU cc_start: 0.9217 (mt) cc_final: 0.9011 (mt) REVERT: A 902 HIS cc_start: 0.8307 (p90) cc_final: 0.7275 (t-90) REVERT: A 994 LEU cc_start: 0.8928 (tp) cc_final: 0.8605 (tp) REVERT: A 1010 ASP cc_start: 0.8468 (m-30) cc_final: 0.7910 (p0) REVERT: B 158 LEU cc_start: 0.9005 (mt) cc_final: 0.8511 (tp) REVERT: B 197 PHE cc_start: 0.7844 (m-10) cc_final: 0.7401 (m-80) REVERT: B 274 MET cc_start: 0.8265 (mmm) cc_final: 0.7766 (mmm) REVERT: B 732 ILE cc_start: 0.8947 (mt) cc_final: 0.8746 (pt) REVERT: B 770 MET cc_start: 0.6732 (tmm) cc_final: 0.6326 (tmm) REVERT: B 808 MET cc_start: 0.6876 (mtm) cc_final: 0.5911 (mpp) REVERT: B 970 PHE cc_start: 0.7561 (p90) cc_final: 0.6531 (p90) REVERT: B 972 PHE cc_start: 0.8714 (m-80) cc_final: 0.8342 (m-80) REVERT: B 994 LEU cc_start: 0.8702 (mt) cc_final: 0.8448 (mt) REVERT: B 1002 LEU cc_start: 0.9149 (tp) cc_final: 0.8277 (tp) REVERT: B 1005 TRP cc_start: 0.7812 (m100) cc_final: 0.7070 (m100) REVERT: C 106 LYS cc_start: 0.9439 (mttt) cc_final: 0.8950 (tttt) REVERT: C 184 MET cc_start: 0.8721 (ttm) cc_final: 0.8322 (tpp) REVERT: C 213 PHE cc_start: 0.7756 (t80) cc_final: 0.7398 (t80) REVERT: C 317 LEU cc_start: 0.9278 (mt) cc_final: 0.9042 (mt) REVERT: C 321 LEU cc_start: 0.9113 (tp) cc_final: 0.8904 (tt) REVERT: C 401 VAL cc_start: 0.9541 (t) cc_final: 0.9290 (t) REVERT: C 487 TYR cc_start: 0.8517 (m-80) cc_final: 0.8031 (m-80) REVERT: C 550 ASN cc_start: 0.8937 (m-40) cc_final: 0.8469 (m-40) REVERT: C 576 GLU cc_start: 0.9375 (tt0) cc_final: 0.8862 (tt0) REVERT: C 597 ASP cc_start: 0.9021 (m-30) cc_final: 0.8763 (m-30) REVERT: C 599 PHE cc_start: 0.9180 (m-80) cc_final: 0.8870 (m-80) REVERT: C 765 LEU cc_start: 0.8185 (tp) cc_final: 0.7909 (tt) REVERT: C 792 LYS cc_start: 0.7612 (mttt) cc_final: 0.7147 (ttpp) REVERT: C 970 PHE cc_start: 0.9511 (p90) cc_final: 0.9262 (p90) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.3090 time to fit residues: 148.9991 Evaluate side-chains 232 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 154 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 132 optimal weight: 0.0980 chunk 48 optimal weight: 0.3980 chunk 192 optimal weight: 0.1980 chunk 212 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 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 = 0.3717 r_free = 0.3717 target = 0.081572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.060820 restraints weight = 118950.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.062747 restraints weight = 72067.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.064035 restraints weight = 51279.081| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.5988 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= 0.106 Angle : 0.590 11.617 29697 Z= 0.300 Chirality : 0.039 0.176 3420 Planarity : 0.003 0.044 3765 Dihedral : 4.672 30.829 2871 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2700 helix: 1.55 (0.16), residues: 1182 sheet: -0.03 (0.29), residues: 303 loop : -1.46 (0.19), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 954 HIS 0.008 0.001 HIS A 744 PHE 0.018 0.001 PHE C 957 TYR 0.015 0.001 TYR C 594 ARG 0.005 0.000 ARG C 691 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 931) hydrogen bonds : angle 4.20732 ( 2601) covalent geometry : bond 0.00225 (22011) covalent geometry : angle 0.58970 (29697) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 2.605 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: A 321 LEU cc_start: 0.9200 (tp) cc_final: 0.8876 (tt) REVERT: A 339 LEU cc_start: 0.9317 (mm) cc_final: 0.9117 (mm) REVERT: A 388 ARG cc_start: 0.9142 (mtt180) cc_final: 0.8747 (mtt-85) REVERT: A 503 ARG cc_start: 0.9237 (mtp85) cc_final: 0.8626 (ttm110) REVERT: A 611 PHE cc_start: 0.8084 (m-80) cc_final: 0.7733 (m-80) REVERT: A 755 LEU cc_start: 0.9116 (pp) cc_final: 0.8780 (tt) REVERT: A 770 MET cc_start: 0.7904 (mmm) cc_final: 0.7668 (mmp) REVERT: A 793 MET cc_start: 0.6564 (mmm) cc_final: 0.6118 (mmm) REVERT: A 808 MET cc_start: 0.8142 (tmm) cc_final: 0.7222 (ttp) REVERT: A 826 GLN cc_start: 0.8938 (mp10) cc_final: 0.8533 (mp10) REVERT: A 875 MET cc_start: 0.7937 (tmm) cc_final: 0.7324 (mtm) REVERT: A 902 HIS cc_start: 0.8346 (p90) cc_final: 0.7514 (p90) REVERT: A 994 LEU cc_start: 0.8949 (tp) cc_final: 0.8622 (tp) REVERT: A 1010 ASP cc_start: 0.8441 (m-30) cc_final: 0.7894 (p0) REVERT: B 197 PHE cc_start: 0.7843 (m-10) cc_final: 0.7372 (m-80) REVERT: B 274 MET cc_start: 0.8236 (mmm) cc_final: 0.7722 (mmm) REVERT: B 562 TYR cc_start: 0.8301 (t80) cc_final: 0.7842 (t80) REVERT: B 770 MET cc_start: 0.6699 (tmm) cc_final: 0.6313 (tmm) REVERT: B 808 MET cc_start: 0.6877 (mtm) cc_final: 0.5933 (mpp) REVERT: B 970 PHE cc_start: 0.7489 (p90) cc_final: 0.6899 (p90) REVERT: B 994 LEU cc_start: 0.8612 (mt) cc_final: 0.8379 (mt) REVERT: B 1002 LEU cc_start: 0.9139 (tp) cc_final: 0.8341 (tp) REVERT: B 1005 TRP cc_start: 0.7829 (m100) cc_final: 0.7320 (m100) REVERT: C 106 LYS cc_start: 0.9448 (mttt) cc_final: 0.8927 (tttt) REVERT: C 184 MET cc_start: 0.8654 (ttm) cc_final: 0.8280 (tpp) REVERT: C 213 PHE cc_start: 0.7731 (t80) cc_final: 0.7337 (t80) REVERT: C 321 LEU cc_start: 0.9189 (tp) cc_final: 0.8890 (tt) REVERT: C 401 VAL cc_start: 0.9523 (t) cc_final: 0.9260 (t) REVERT: C 487 TYR cc_start: 0.8494 (m-80) cc_final: 0.8069 (m-80) REVERT: C 576 GLU cc_start: 0.9356 (tt0) cc_final: 0.9065 (tt0) REVERT: C 597 ASP cc_start: 0.9034 (m-30) cc_final: 0.8750 (m-30) REVERT: C 714 ILE cc_start: 0.9121 (tp) cc_final: 0.8893 (tp) REVERT: C 792 LYS cc_start: 0.7530 (mttt) cc_final: 0.7041 (ttpp) REVERT: C 875 MET cc_start: 0.7983 (pmm) cc_final: 0.7632 (pmm) REVERT: C 917 TRP cc_start: 0.5263 (p90) cc_final: 0.5027 (p90) REVERT: C 970 PHE cc_start: 0.9502 (p90) cc_final: 0.9233 (p90) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.3037 time to fit residues: 153.7679 Evaluate side-chains 234 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 222 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 7 optimal weight: 0.0980 chunk 199 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 overall best weight: 2.6188 ------------------------------------------------------------------------------- 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 B 162 GLN B 286 HIS ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 HIS B 800 HIS C 147 HIS ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1006 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.079010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.058335 restraints weight = 119460.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.060160 restraints weight = 73017.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.061395 restraints weight = 52264.464| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22011 Z= 0.182 Angle : 0.670 12.996 29697 Z= 0.344 Chirality : 0.041 0.192 3420 Planarity : 0.004 0.050 3765 Dihedral : 4.998 30.857 2871 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.17), residues: 2700 helix: 1.24 (0.16), residues: 1170 sheet: -0.19 (0.30), residues: 276 loop : -1.57 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 954 HIS 0.008 0.001 HIS A 601 PHE 0.020 0.002 PHE B 202 TYR 0.019 0.002 TYR C 594 ARG 0.005 0.001 ARG C 691 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 931) hydrogen bonds : angle 4.56635 ( 2601) covalent geometry : bond 0.00387 (22011) covalent geometry : angle 0.67029 (29697) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 2.449 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 321 LEU cc_start: 0.9225 (tp) cc_final: 0.8888 (tt) REVERT: A 388 ARG cc_start: 0.9136 (mtt180) cc_final: 0.8732 (mtt-85) REVERT: A 503 ARG cc_start: 0.9234 (mtp85) cc_final: 0.8641 (ttm110) REVERT: A 605 CYS cc_start: 0.8536 (m) cc_final: 0.7157 (t) REVERT: A 611 PHE cc_start: 0.8131 (m-80) cc_final: 0.7718 (m-80) REVERT: A 755 LEU cc_start: 0.9141 (pp) cc_final: 0.8816 (tt) REVERT: A 770 MET cc_start: 0.8242 (mmm) cc_final: 0.7783 (mmp) REVERT: A 793 MET cc_start: 0.6570 (mmm) cc_final: 0.6146 (mmm) REVERT: A 875 MET cc_start: 0.7918 (tmm) cc_final: 0.7116 (mtm) REVERT: A 902 HIS cc_start: 0.8242 (p90) cc_final: 0.7485 (p90) REVERT: A 994 LEU cc_start: 0.8912 (tp) cc_final: 0.8587 (tp) REVERT: A 1010 ASP cc_start: 0.8566 (m-30) cc_final: 0.8138 (p0) REVERT: B 158 LEU cc_start: 0.8679 (mp) cc_final: 0.8001 (tp) REVERT: B 274 MET cc_start: 0.8353 (mmm) cc_final: 0.7909 (mmm) REVERT: B 770 MET cc_start: 0.6816 (tmm) cc_final: 0.6394 (tmm) REVERT: B 1002 LEU cc_start: 0.9094 (tp) cc_final: 0.8125 (tp) REVERT: B 1005 TRP cc_start: 0.8015 (m100) cc_final: 0.7241 (m100) REVERT: C 106 LYS cc_start: 0.9488 (mttt) cc_final: 0.9020 (tttt) REVERT: C 184 MET cc_start: 0.8774 (ttm) cc_final: 0.8372 (tpp) REVERT: C 317 LEU cc_start: 0.9252 (mt) cc_final: 0.8991 (mt) REVERT: C 321 LEU cc_start: 0.9196 (tp) cc_final: 0.8882 (tt) REVERT: C 401 VAL cc_start: 0.9589 (t) cc_final: 0.9388 (t) REVERT: C 487 TYR cc_start: 0.8530 (m-80) cc_final: 0.7928 (m-80) REVERT: C 550 ASN cc_start: 0.9060 (m-40) cc_final: 0.8633 (m-40) REVERT: C 597 ASP cc_start: 0.8999 (m-30) cc_final: 0.8769 (m-30) REVERT: C 599 PHE cc_start: 0.9164 (m-80) cc_final: 0.8764 (m-80) REVERT: C 749 GLN cc_start: 0.5020 (mt0) cc_final: 0.4392 (pt0) REVERT: C 912 LEU cc_start: 0.9337 (mp) cc_final: 0.8928 (mp) REVERT: C 917 TRP cc_start: 0.5361 (p90) cc_final: 0.5100 (p90) REVERT: C 970 PHE cc_start: 0.9529 (p90) cc_final: 0.9275 (p90) REVERT: C 1019 PHE cc_start: 0.7894 (t80) cc_final: 0.7655 (t80) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.3122 time to fit residues: 140.7758 Evaluate side-chains 207 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 60 optimal weight: 30.0000 chunk 140 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 204 optimal weight: 0.0170 chunk 46 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 13 optimal weight: 0.0070 chunk 38 optimal weight: 6.9990 chunk 223 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- 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 B 147 HIS B 162 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 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 = 0.3713 r_free = 0.3713 target = 0.081259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.060444 restraints weight = 118738.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.062312 restraints weight = 72755.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.063564 restraints weight = 52150.538| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.6478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22011 Z= 0.107 Angle : 0.616 12.285 29697 Z= 0.313 Chirality : 0.040 0.192 3420 Planarity : 0.003 0.046 3765 Dihedral : 4.780 30.307 2871 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2700 helix: 1.46 (0.16), residues: 1185 sheet: -0.14 (0.29), residues: 300 loop : -1.54 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 888 HIS 0.009 0.001 HIS A 744 PHE 0.021 0.001 PHE B 232 TYR 0.011 0.001 TYR A 859 ARG 0.005 0.000 ARG B 329 Details of bonding type rmsd hydrogen bonds : bond 0.03056 ( 931) hydrogen bonds : angle 4.30808 ( 2601) covalent geometry : bond 0.00225 (22011) covalent geometry : angle 0.61644 (29697) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 2.491 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 321 LEU cc_start: 0.9196 (tp) cc_final: 0.8856 (tt) REVERT: A 388 ARG cc_start: 0.9136 (mtt180) cc_final: 0.8872 (mtt90) REVERT: A 503 ARG cc_start: 0.9160 (mtp85) cc_final: 0.8921 (ttm110) REVERT: A 611 PHE cc_start: 0.8113 (m-80) cc_final: 0.7649 (m-80) REVERT: A 755 LEU cc_start: 0.9110 (pp) cc_final: 0.8815 (tt) REVERT: A 775 MET cc_start: 0.7467 (ppp) cc_final: 0.7198 (ppp) REVERT: A 793 MET cc_start: 0.6472 (mmm) cc_final: 0.6015 (mmm) REVERT: A 826 GLN cc_start: 0.8926 (mp10) cc_final: 0.8637 (mp10) REVERT: A 875 MET cc_start: 0.7944 (tmm) cc_final: 0.7279 (mtm) REVERT: A 902 HIS cc_start: 0.8288 (p90) cc_final: 0.7488 (p90) REVERT: A 994 LEU cc_start: 0.8914 (tp) cc_final: 0.8604 (tp) REVERT: B 197 PHE cc_start: 0.7971 (m-10) cc_final: 0.7556 (m-80) REVERT: B 274 MET cc_start: 0.8242 (mmm) cc_final: 0.7782 (mmm) REVERT: B 335 MET cc_start: 0.8012 (tmm) cc_final: 0.7768 (tmm) REVERT: B 562 TYR cc_start: 0.8386 (t80) cc_final: 0.7910 (t80) REVERT: B 770 MET cc_start: 0.6637 (tmm) cc_final: 0.6403 (tmm) REVERT: B 1002 LEU cc_start: 0.9105 (tp) cc_final: 0.8196 (tp) REVERT: B 1005 TRP cc_start: 0.7834 (m100) cc_final: 0.7430 (m100) REVERT: C 106 LYS cc_start: 0.9496 (mttt) cc_final: 0.9057 (mmmt) REVERT: C 184 MET cc_start: 0.8666 (ttm) cc_final: 0.8281 (tpp) REVERT: C 321 LEU cc_start: 0.9173 (tp) cc_final: 0.8932 (tp) REVERT: C 401 VAL cc_start: 0.9504 (t) cc_final: 0.9245 (t) REVERT: C 487 TYR cc_start: 0.8457 (m-80) cc_final: 0.8025 (m-80) REVERT: C 550 ASN cc_start: 0.9050 (m-40) cc_final: 0.8602 (m-40) REVERT: C 576 GLU cc_start: 0.9367 (tt0) cc_final: 0.9145 (tt0) REVERT: C 597 ASP cc_start: 0.8999 (m-30) cc_final: 0.8770 (m-30) REVERT: C 599 PHE cc_start: 0.9092 (m-80) cc_final: 0.8629 (m-80) REVERT: C 714 ILE cc_start: 0.9105 (tp) cc_final: 0.8867 (tp) REVERT: C 727 GLU cc_start: 0.8188 (pm20) cc_final: 0.7881 (pp20) REVERT: C 875 MET cc_start: 0.7886 (pmm) cc_final: 0.7479 (pmm) REVERT: C 917 TRP cc_start: 0.5306 (p90) cc_final: 0.5087 (p90) REVERT: C 970 PHE cc_start: 0.9486 (p90) cc_final: 0.9224 (p90) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.2947 time to fit residues: 134.5825 Evaluate side-chains 220 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 176 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 192 optimal weight: 0.0170 chunk 137 optimal weight: 0.7980 chunk 242 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- 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 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.080270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.059413 restraints weight = 117621.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.061233 restraints weight = 72436.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.062467 restraints weight = 51877.387| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.6661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22011 Z= 0.133 Angle : 0.645 12.363 29697 Z= 0.328 Chirality : 0.041 0.286 3420 Planarity : 0.004 0.068 3765 Dihedral : 4.814 29.531 2871 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.17), residues: 2700 helix: 1.41 (0.16), residues: 1185 sheet: -0.40 (0.29), residues: 309 loop : -1.58 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 888 HIS 0.008 0.001 HIS A 744 PHE 0.021 0.001 PHE B 232 TYR 0.014 0.001 TYR C 367 ARG 0.017 0.001 ARG B 691 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 931) hydrogen bonds : angle 4.38306 ( 2601) covalent geometry : bond 0.00284 (22011) covalent geometry : angle 0.64492 (29697) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 2.907 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: A 321 LEU cc_start: 0.9208 (tp) cc_final: 0.8845 (tt) REVERT: A 388 ARG cc_start: 0.9130 (mtt180) cc_final: 0.8732 (mtt-85) REVERT: A 503 ARG cc_start: 0.9164 (mtp85) cc_final: 0.8556 (ttm110) REVERT: A 579 PHE cc_start: 0.9099 (m-10) cc_final: 0.8510 (m-80) REVERT: A 611 PHE cc_start: 0.8033 (m-80) cc_final: 0.7656 (m-80) REVERT: A 755 LEU cc_start: 0.9123 (pp) cc_final: 0.8821 (tt) REVERT: A 775 MET cc_start: 0.7430 (ppp) cc_final: 0.7147 (ppp) REVERT: A 793 MET cc_start: 0.6418 (mmm) cc_final: 0.5944 (mmm) REVERT: A 826 GLN cc_start: 0.8904 (mp10) cc_final: 0.8635 (mp10) REVERT: A 875 MET cc_start: 0.7937 (tmm) cc_final: 0.7261 (mtm) REVERT: A 902 HIS cc_start: 0.8305 (p90) cc_final: 0.7514 (p90) REVERT: A 994 LEU cc_start: 0.8937 (tp) cc_final: 0.8652 (tp) REVERT: B 274 MET cc_start: 0.8276 (mmm) cc_final: 0.7849 (mmm) REVERT: B 562 TYR cc_start: 0.8463 (t80) cc_final: 0.7996 (t80) REVERT: B 770 MET cc_start: 0.6659 (tmm) cc_final: 0.6340 (tmm) REVERT: B 1002 LEU cc_start: 0.9059 (tp) cc_final: 0.7970 (tp) REVERT: B 1005 TRP cc_start: 0.7891 (m100) cc_final: 0.7455 (m100) REVERT: C 106 LYS cc_start: 0.9506 (mttt) cc_final: 0.9094 (mmmt) REVERT: C 184 MET cc_start: 0.8694 (ttm) cc_final: 0.8314 (tpp) REVERT: C 317 LEU cc_start: 0.9186 (mt) cc_final: 0.8965 (mt) REVERT: C 321 LEU cc_start: 0.9185 (tp) cc_final: 0.8841 (tt) REVERT: C 401 VAL cc_start: 0.9550 (t) cc_final: 0.9326 (t) REVERT: C 487 TYR cc_start: 0.8478 (m-80) cc_final: 0.8026 (m-80) REVERT: C 550 ASN cc_start: 0.9030 (m-40) cc_final: 0.8568 (m-40) REVERT: C 597 ASP cc_start: 0.8946 (m-30) cc_final: 0.8723 (m-30) REVERT: C 599 PHE cc_start: 0.9093 (m-80) cc_final: 0.8600 (m-80) REVERT: C 692 LEU cc_start: 0.9528 (tt) cc_final: 0.9317 (tt) REVERT: C 714 ILE cc_start: 0.9144 (tp) cc_final: 0.8911 (tp) REVERT: C 875 MET cc_start: 0.8001 (pmm) cc_final: 0.7647 (pmm) REVERT: C 912 LEU cc_start: 0.9373 (mp) cc_final: 0.9122 (mp) REVERT: C 917 TRP cc_start: 0.5361 (p90) cc_final: 0.4896 (p90) REVERT: C 970 PHE cc_start: 0.9501 (p90) cc_final: 0.9243 (p90) REVERT: C 1019 PHE cc_start: 0.7768 (t80) cc_final: 0.7527 (t80) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.3357 time to fit residues: 147.2863 Evaluate side-chains 210 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 49 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 139 optimal weight: 0.7980 chunk 173 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 B 162 GLN B 433 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN ** C 657 GLN ** 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 = 0.3658 r_free = 0.3658 target = 0.078668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.057891 restraints weight = 119903.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.059588 restraints weight = 76192.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.060744 restraints weight = 55959.770| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.7007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22011 Z= 0.181 Angle : 0.707 13.052 29697 Z= 0.361 Chirality : 0.042 0.207 3420 Planarity : 0.004 0.068 3765 Dihedral : 5.218 30.974 2871 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2700 helix: 1.22 (0.16), residues: 1167 sheet: -0.39 (0.30), residues: 279 loop : -1.61 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 888 HIS 0.009 0.001 HIS A 744 PHE 0.022 0.002 PHE A 957 TYR 0.018 0.002 TYR C 367 ARG 0.019 0.001 ARG B 691 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 931) hydrogen bonds : angle 4.70121 ( 2601) covalent geometry : bond 0.00387 (22011) covalent geometry : angle 0.70651 (29697) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8929.56 seconds wall clock time: 158 minutes 13.85 seconds (9493.85 seconds total)