Starting phenix.real_space_refine on Wed May 21 18:55:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fw9_29498/05_2025/8fw9_29498_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fw9_29498/05_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_29498/05_2025/8fw9_29498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fw9_29498/05_2025/8fw9_29498.map" model { file = "/net/cci-nas-00/data/ceres_data/8fw9_29498/05_2025/8fw9_29498_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fw9_29498/05_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-5687/modules/chem_data/mon_lib" Total number of atoms: 21612 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7204 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Chain: "B" Number of atoms: 7204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7204 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Chain: "C" Number of atoms: 7204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7204 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Time building chain proxies: 13.36, per 1000 atoms: 0.62 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: 5.39 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: 3.37 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: 9.45 Time building geometry restraints manager: 6.38 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: 9.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.970 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 51.540 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.500 ------------------------------------------------------------------------------- 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 : 2.424 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: 0.3727 time to fit residues: 362.7709 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 : 2.491 ------------------------------------------------------------------------------- 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 = 0.085455 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 = 113238.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.066446 restraints weight = 66338.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.067925 restraints weight = 45614.206| |-----------------------------------------------------------------------------| 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 : 2.330 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: 0.8546 (tmm) REVERT: A 233 MET cc_start: 0.8871 (mmt) cc_final: 0.8127 (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: 0.8684 (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: 0.7117 (p90) cc_final: 0.6867 (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: 0.7627 (m-10) REVERT: A 755 LEU cc_start: 0.9172 (pp) cc_final: 0.8804 (tt) REVERT: A 793 MET cc_start: 0.6661 (mmm) cc_final: 0.6102 (mmm) REVERT: B 114 PHE cc_start: 0.8224 (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: 0.9086 (mm) cc_final: 0.8682 (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: 0.9476 (mp) cc_final: 0.9242 (tt) REVERT: B 732 ILE cc_start: 0.8806 (mt) cc_final: 0.8568 (pt) REVERT: B 770 MET cc_start: 0.7034 (tmm) cc_final: 0.6569 (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: 0.5892 (mtt) cc_final: 0.4485 (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: 0.8165 (mp0) cc_final: 0.7908 (tp30) REVERT: C 215 THR cc_start: 0.9280 (m) cc_final: 0.9001 (p) REVERT: C 248 ASP cc_start: 0.8409 (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: 0.9108 (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: 0.3238 time to fit residues: 230.5880 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 : 2.463 ------------------------------------------------------------------------------- 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: 9.9990 chunk 233 optimal weight: 0.0050 chunk 265 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 147 HIS ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.082181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.061053 restraints weight = 115045.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.063023 restraints weight = 68899.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.064368 restraints weight = 48540.261| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22011 Z= 0.159 Angle : 0.647 15.363 29697 Z= 0.338 Chirality : 0.040 0.194 3420 Planarity : 0.004 0.056 3765 Dihedral : 4.907 34.140 2871 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.03 % Twisted General : 0.04 % Rama-Z (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: 0.08 (0.17), residues: 2700 helix: 1.31 (0.16), residues: 1161 sheet: -0.04 (0.28), residues: 309 loop : -1.16 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 917 HIS 0.008 0.001 HIS A 744 PHE 0.024 0.002 PHE B 957 TYR 0.018 0.002 TYR C 250 ARG 0.007 0.001 ARG C 503 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 931) hydrogen bonds : angle 4.73736 ( 2601) covalent geometry : bond 0.00331 (22011) covalent geometry : angle 0.64716 (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 350 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7960 (pp20) cc_final: 0.7753 (pm20) REVERT: A 197 PHE cc_start: 0.8571 (m-80) cc_final: 0.8243 (m-80) REVERT: A 321 LEU cc_start: 0.9164 (tp) cc_final: 0.8837 (tt) REVERT: A 503 ARG cc_start: 0.9120 (mtp85) cc_final: 0.8834 (mtp85) REVERT: A 755 LEU cc_start: 0.9157 (pp) cc_final: 0.8861 (tt) REVERT: A 793 MET cc_start: 0.6481 (mmm) cc_final: 0.6198 (mmm) REVERT: A 902 HIS cc_start: 0.8376 (p90) cc_final: 0.7951 (p-80) REVERT: B 158 LEU cc_start: 0.8992 (mt) cc_final: 0.8490 (tp) REVERT: B 274 MET cc_start: 0.8331 (mmm) cc_final: 0.7722 (mmm) REVERT: B 477 MET cc_start: 0.6270 (mmm) cc_final: 0.6017 (mmm) REVERT: B 562 TYR cc_start: 0.8229 (t80) cc_final: 0.7826 (t80) REVERT: B 584 LEU cc_start: 0.9353 (tp) cc_final: 0.9134 (tp) REVERT: B 612 ILE cc_start: 0.7747 (mm) cc_final: 0.7471 (mm) REVERT: B 680 LEU cc_start: 0.9306 (mt) cc_final: 0.9047 (mt) REVERT: B 729 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8232 (tp30) REVERT: B 808 MET cc_start: 0.5578 (mtt) cc_final: 0.4200 (mpp) REVERT: B 969 PHE cc_start: 0.8744 (p90) cc_final: 0.8518 (p90) REVERT: C 106 LYS cc_start: 0.9398 (mttt) cc_final: 0.8960 (mmmt) REVERT: C 122 GLU cc_start: 0.8287 (mp0) cc_final: 0.7866 (tp30) REVERT: C 184 MET cc_start: 0.8729 (ttm) cc_final: 0.8376 (tpp) REVERT: C 321 LEU cc_start: 0.9159 (tp) cc_final: 0.8958 (tt) REVERT: C 337 THR cc_start: 0.9126 (m) cc_final: 0.8828 (p) REVERT: C 401 VAL cc_start: 0.9535 (t) cc_final: 0.9301 (t) REVERT: C 487 TYR cc_start: 0.8499 (m-80) cc_final: 0.8076 (m-80) REVERT: C 571 LEU cc_start: 0.9587 (mm) cc_final: 0.9321 (mt) REVERT: C 576 GLU cc_start: 0.9466 (tt0) cc_final: 0.9197 (tt0) REVERT: C 585 TYR cc_start: 0.7705 (t80) cc_final: 0.7393 (t80) REVERT: C 597 ASP cc_start: 0.9178 (m-30) cc_final: 0.8909 (m-30) REVERT: C 765 LEU cc_start: 0.7989 (tp) cc_final: 0.7611 (tp) REVERT: C 792 LYS cc_start: 0.7490 (mttt) cc_final: 0.7076 (ttpp) REVERT: C 958 MET cc_start: 0.8385 (mmp) cc_final: 0.7993 (mmm) REVERT: C 970 PHE cc_start: 0.9385 (p90) cc_final: 0.9094 (p90) REVERT: C 1019 PHE cc_start: 0.7538 (t80) cc_final: 0.7309 (t80) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.3042 time to fit residues: 168.6488 Evaluate side-chains 250 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 2.457 ------------------------------------------------------------------------------- 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: 0.8980 chunk 58 optimal weight: 2.9990 chunk 259 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 chunk 163 optimal weight: 0.0040 chunk 126 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- 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 C 147 HIS ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 ASN C 604 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.082398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.061239 restraints weight = 115444.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.063238 restraints weight = 68494.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.064615 restraints weight = 48121.123| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4921 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= 0.120 Angle : 0.601 11.951 29697 Z= 0.311 Chirality : 0.039 0.197 3420 Planarity : 0.004 0.052 3765 Dihedral : 4.803 33.584 2871 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: 0.06 (0.17), residues: 2700 helix: 1.39 (0.16), residues: 1167 sheet: 0.06 (0.28), residues: 306 loop : -1.33 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 954 HIS 0.015 0.001 HIS A 744 PHE 0.021 0.002 PHE B 957 TYR 0.015 0.001 TYR C 250 ARG 0.009 0.000 ARG C 691 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 931) hydrogen bonds : angle 4.48071 ( 2601) covalent geometry : bond 0.00254 (22011) covalent geometry : angle 0.60067 (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 336 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 2.349 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 95 GLU cc_start: 0.8045 (pp20) cc_final: 0.7836 (pm20) REVERT: A 197 PHE cc_start: 0.8683 (m-80) cc_final: 0.8446 (m-80) REVERT: A 257 ASN cc_start: 0.8698 (m-40) cc_final: 0.8332 (p0) REVERT: A 388 ARG cc_start: 0.9111 (mtt180) cc_final: 0.8874 (mtt90) REVERT: A 503 ARG cc_start: 0.9274 (mtp85) cc_final: 0.8796 (mtp85) REVERT: A 611 PHE cc_start: 0.7915 (m-80) cc_final: 0.7689 (m-10) REVERT: A 755 LEU cc_start: 0.9145 (pp) cc_final: 0.8837 (tt) REVERT: A 770 MET cc_start: 0.7815 (mmm) cc_final: 0.7593 (mmp) REVERT: A 793 MET cc_start: 0.6444 (mmm) cc_final: 0.6123 (mmm) REVERT: A 826 GLN cc_start: 0.9016 (mp10) cc_final: 0.8618 (mp10) REVERT: A 875 MET cc_start: 0.7908 (tmm) cc_final: 0.6813 (mtm) REVERT: A 899 LEU cc_start: 0.9303 (mt) cc_final: 0.9061 (mt) REVERT: A 902 HIS cc_start: 0.8355 (p90) cc_final: 0.7425 (t-90) REVERT: B 158 LEU cc_start: 0.9014 (mt) cc_final: 0.8520 (tp) REVERT: B 197 PHE cc_start: 0.8055 (m-10) cc_final: 0.7754 (m-10) REVERT: B 274 MET cc_start: 0.8167 (mmm) cc_final: 0.7587 (mmm) REVERT: B 562 TYR cc_start: 0.8256 (t80) cc_final: 0.7784 (t80) REVERT: B 732 ILE cc_start: 0.8906 (mt) cc_final: 0.8680 (pt) REVERT: B 770 MET cc_start: 0.6495 (tmm) cc_final: 0.5989 (tmm) REVERT: B 808 MET cc_start: 0.5387 (mtt) cc_final: 0.4081 (mpp) REVERT: C 106 LYS cc_start: 0.9427 (mttt) cc_final: 0.8886 (mmmt) REVERT: C 122 GLU cc_start: 0.8144 (mp0) cc_final: 0.7818 (tp30) REVERT: C 184 MET cc_start: 0.8736 (ttm) cc_final: 0.8354 (tpp) REVERT: C 337 THR cc_start: 0.9064 (m) cc_final: 0.8798 (p) REVERT: C 401 VAL cc_start: 0.9504 (t) cc_final: 0.9251 (t) REVERT: C 473 TYR cc_start: 0.8282 (m-80) cc_final: 0.7896 (m-80) REVERT: C 487 TYR cc_start: 0.8449 (m-80) cc_final: 0.8049 (m-80) REVERT: C 550 ASN cc_start: 0.8959 (m110) cc_final: 0.8528 (m-40) REVERT: C 571 LEU cc_start: 0.9596 (mm) cc_final: 0.9382 (mt) REVERT: C 597 ASP cc_start: 0.9128 (m-30) cc_final: 0.8852 (m-30) REVERT: C 599 PHE cc_start: 0.9244 (m-80) cc_final: 0.8842 (m-80) REVERT: C 765 LEU cc_start: 0.8018 (tp) cc_final: 0.7661 (tp) REVERT: C 792 LYS cc_start: 0.7498 (mttt) cc_final: 0.7084 (ttpp) REVERT: C 875 MET cc_start: 0.8278 (pmm) cc_final: 0.8009 (pmm) REVERT: C 958 MET cc_start: 0.8355 (mmp) cc_final: 0.7827 (mmm) REVERT: C 970 PHE cc_start: 0.9467 (p90) cc_final: 0.9196 (p90) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.3012 time to fit residues: 160.5016 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 : 2.610 ------------------------------------------------------------------------------- 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: 3.9990 chunk 201 optimal weight: 0.3980 chunk 249 optimal weight: 2.9990 chunk 60 optimal weight: 0.0040 chunk 154 optimal weight: 7.9990 chunk 195 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 179 optimal weight: 0.0170 chunk 168 optimal weight: 20.0000 chunk 219 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.4030 ------------------------------------------------------------------------------- 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 865 ASN B 162 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 772 ASN C 147 HIS C 508 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.083417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.062113 restraints weight = 113795.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.064115 restraints weight = 68179.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.065475 restraints weight = 47866.814| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22011 Z= 0.100 Angle : 0.583 11.566 29697 Z= 0.297 Chirality : 0.039 0.182 3420 Planarity : 0.003 0.044 3765 Dihedral : 4.595 31.331 2871 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: 0.06 (0.17), residues: 2700 helix: 1.40 (0.16), residues: 1197 sheet: -0.06 (0.28), residues: 318 loop : -1.39 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 954 HIS 0.005 0.001 HIS A 601 PHE 0.020 0.001 PHE B 957 TYR 0.022 0.001 TYR A 715 ARG 0.007 0.000 ARG C 691 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 931) hydrogen bonds : angle 4.23853 ( 2601) covalent geometry : bond 0.00208 (22011) covalent geometry : angle 0.58257 (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 329 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 2.364 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: A 388 ARG cc_start: 0.9113 (mtt180) cc_final: 0.8854 (mtt90) REVERT: A 474 LEU cc_start: 0.9388 (tp) cc_final: 0.9160 (pp) REVERT: A 503 ARG cc_start: 0.9198 (mtp85) cc_final: 0.8634 (ttm110) REVERT: A 611 PHE cc_start: 0.7904 (m-80) cc_final: 0.7676 (m-10) REVERT: A 755 LEU cc_start: 0.9251 (pp) cc_final: 0.8902 (tt) REVERT: A 793 MET cc_start: 0.6426 (mmm) cc_final: 0.6063 (mmm) REVERT: A 826 GLN cc_start: 0.8981 (mp10) cc_final: 0.8705 (mp10) REVERT: A 831 CYS cc_start: 0.8189 (m) cc_final: 0.7477 (m) REVERT: A 875 MET cc_start: 0.7755 (tmm) cc_final: 0.6659 (mtm) REVERT: A 899 LEU cc_start: 0.9274 (mt) cc_final: 0.9030 (mt) REVERT: A 902 HIS cc_start: 0.8328 (p90) cc_final: 0.7305 (t-90) REVERT: B 158 LEU cc_start: 0.8969 (mt) cc_final: 0.8503 (tp) REVERT: B 197 PHE cc_start: 0.7925 (m-10) cc_final: 0.7604 (m-10) REVERT: B 274 MET cc_start: 0.8185 (mmm) cc_final: 0.7677 (mmm) REVERT: B 313 LEU cc_start: 0.7522 (tp) cc_final: 0.7298 (tp) REVERT: B 714 ILE cc_start: 0.8651 (pt) cc_final: 0.8386 (tp) REVERT: B 717 LEU cc_start: 0.9496 (mm) cc_final: 0.9135 (mm) REVERT: B 732 ILE cc_start: 0.8885 (mt) cc_final: 0.8659 (pt) REVERT: B 770 MET cc_start: 0.6438 (tmm) cc_final: 0.6061 (tmm) REVERT: B 808 MET cc_start: 0.5318 (mtt) cc_final: 0.4050 (mpp) REVERT: B 970 PHE cc_start: 0.7336 (p90) cc_final: 0.6227 (p90) REVERT: B 1002 LEU cc_start: 0.9200 (tp) cc_final: 0.8599 (tp) REVERT: C 106 LYS cc_start: 0.9452 (mttt) cc_final: 0.8994 (mmmt) REVERT: C 184 MET cc_start: 0.8598 (ttm) cc_final: 0.8263 (tpp) REVERT: C 213 PHE cc_start: 0.7645 (t80) cc_final: 0.7294 (t80) REVERT: C 215 THR cc_start: 0.9336 (m) cc_final: 0.9102 (p) REVERT: C 244 LEU cc_start: 0.8980 (mt) cc_final: 0.8573 (mp) REVERT: C 401 VAL cc_start: 0.9454 (t) cc_final: 0.9208 (t) REVERT: C 487 TYR cc_start: 0.8277 (m-80) cc_final: 0.7965 (m-80) REVERT: C 597 ASP cc_start: 0.9050 (m-30) cc_final: 0.8758 (m-30) REVERT: C 765 LEU cc_start: 0.8024 (tp) cc_final: 0.7680 (tp) REVERT: C 792 LYS cc_start: 0.7444 (mttt) cc_final: 0.7053 (ttpp) REVERT: C 970 PHE cc_start: 0.9449 (p90) cc_final: 0.9120 (p90) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.2974 time to fit residues: 156.0959 Evaluate side-chains 248 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 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: 6.9990 chunk 246 optimal weight: 8.9990 chunk 249 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 186 optimal weight: 0.0050 chunk 201 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 overall best weight: 2.7400 ------------------------------------------------------------------------------- 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 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS C 550 ASN ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.079623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.058613 restraints weight = 118852.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.060415 restraints weight = 73154.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.061644 restraints weight = 52720.584| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22011 Z= 0.194 Angle : 0.677 12.832 29697 Z= 0.350 Chirality : 0.041 0.206 3420 Planarity : 0.004 0.052 3765 Dihedral : 4.976 31.685 2871 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.23 (0.17), residues: 2700 helix: 1.22 (0.16), residues: 1185 sheet: -0.14 (0.29), residues: 309 loop : -1.60 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 186 HIS 0.010 0.001 HIS A 744 PHE 0.028 0.002 PHE A 408 TYR 0.020 0.002 TYR A 715 ARG 0.005 0.001 ARG C 691 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 931) hydrogen bonds : angle 4.60499 ( 2601) covalent geometry : bond 0.00414 (22011) covalent geometry : angle 0.67743 (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 299 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 2.365 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: A 95 GLU cc_start: 0.8177 (pp20) cc_final: 0.7935 (pm20) REVERT: A 197 PHE cc_start: 0.8585 (m-10) cc_final: 0.8367 (m-80) REVERT: A 232 PHE cc_start: 0.9175 (t80) cc_final: 0.8893 (t80) REVERT: A 340 PHE cc_start: 0.9088 (m-10) cc_final: 0.8844 (m-10) REVERT: A 388 ARG cc_start: 0.9126 (mtt180) cc_final: 0.8726 (mtt-85) REVERT: A 503 ARG cc_start: 0.9187 (mtp85) cc_final: 0.8682 (ttm110) REVERT: A 611 PHE cc_start: 0.8103 (m-80) cc_final: 0.7768 (m-10) REVERT: A 755 LEU cc_start: 0.9195 (pp) cc_final: 0.8809 (tt) REVERT: A 793 MET cc_start: 0.6558 (mmm) cc_final: 0.6149 (mmm) REVERT: A 808 MET cc_start: 0.8208 (tmm) cc_final: 0.7155 (ttp) REVERT: A 902 HIS cc_start: 0.8304 (p90) cc_final: 0.7979 (p-80) REVERT: A 952 ASP cc_start: 0.8737 (t0) cc_final: 0.8473 (p0) REVERT: A 994 LEU cc_start: 0.8821 (tp) cc_final: 0.8485 (tp) REVERT: A 1010 ASP cc_start: 0.8486 (m-30) cc_final: 0.7970 (p0) REVERT: B 158 LEU cc_start: 0.9071 (mt) cc_final: 0.8553 (tp) REVERT: B 197 PHE cc_start: 0.8188 (m-10) cc_final: 0.7855 (m-80) REVERT: B 274 MET cc_start: 0.8330 (mmm) cc_final: 0.7784 (mmm) REVERT: B 562 TYR cc_start: 0.8530 (t80) cc_final: 0.8172 (t80) REVERT: B 599 PHE cc_start: 0.9243 (m-80) cc_final: 0.8853 (m-80) REVERT: B 770 MET cc_start: 0.6789 (tmm) cc_final: 0.6332 (tmm) REVERT: B 994 LEU cc_start: 0.8729 (mt) cc_final: 0.8468 (mt) REVERT: B 1002 LEU cc_start: 0.9146 (tp) cc_final: 0.8115 (tp) REVERT: B 1005 TRP cc_start: 0.8095 (m100) cc_final: 0.7066 (m100) REVERT: C 106 LYS cc_start: 0.9491 (mttt) cc_final: 0.9018 (tttt) REVERT: C 184 MET cc_start: 0.8767 (ttm) cc_final: 0.8373 (tpp) REVERT: C 213 PHE cc_start: 0.7792 (t80) cc_final: 0.7466 (t80) REVERT: C 401 VAL cc_start: 0.9606 (t) cc_final: 0.9374 (t) REVERT: C 487 TYR cc_start: 0.8628 (m-80) cc_final: 0.8009 (m-80) REVERT: C 550 ASN cc_start: 0.8992 (m110) cc_final: 0.8569 (m-40) REVERT: C 597 ASP cc_start: 0.9083 (m-30) cc_final: 0.8846 (m-30) REVERT: C 599 PHE cc_start: 0.9231 (m-80) cc_final: 0.8831 (m-80) REVERT: C 765 LEU cc_start: 0.8009 (tp) cc_final: 0.7686 (tp) REVERT: C 775 MET cc_start: 0.8669 (ppp) cc_final: 0.8300 (ppp) REVERT: C 792 LYS cc_start: 0.7803 (mttt) cc_final: 0.7349 (ttpt) REVERT: C 793 MET cc_start: 0.6777 (mmm) cc_final: 0.6427 (mmm) REVERT: C 970 PHE cc_start: 0.9475 (p90) cc_final: 0.9230 (p90) REVERT: C 999 GLU cc_start: 0.7969 (tp30) cc_final: 0.7395 (tp30) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3144 time to fit residues: 149.5907 Evaluate side-chains 222 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 2.411 ------------------------------------------------------------------------------- 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: 0.7980 chunk 140 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 357 HIS ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS C 147 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.080501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.059760 restraints weight = 117276.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.061586 restraints weight = 72003.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.062830 restraints weight = 51694.444| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22011 Z= 0.139 Angle : 0.628 12.473 29697 Z= 0.323 Chirality : 0.040 0.188 3420 Planarity : 0.004 0.052 3765 Dihedral : 4.920 31.060 2871 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: -0.14 (0.17), residues: 2700 helix: 1.29 (0.16), residues: 1185 sheet: -0.05 (0.29), residues: 303 loop : -1.55 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 186 HIS 0.008 0.001 HIS A 744 PHE 0.024 0.002 PHE A 114 TYR 0.018 0.001 TYR A 715 ARG 0.005 0.000 ARG C 691 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 931) hydrogen bonds : angle 4.47518 ( 2601) covalent geometry : bond 0.00298 (22011) covalent geometry : angle 0.62821 (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 287 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 2.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.8519 (m-10) cc_final: 0.8281 (m-80) REVERT: A 388 ARG cc_start: 0.9115 (mtt180) cc_final: 0.8709 (mtt-85) REVERT: A 503 ARG cc_start: 0.9216 (mtp85) cc_final: 0.8722 (mtp85) REVERT: A 611 PHE cc_start: 0.8105 (m-80) cc_final: 0.7661 (m-10) REVERT: A 755 LEU cc_start: 0.9148 (pp) cc_final: 0.8808 (tt) REVERT: A 793 MET cc_start: 0.6652 (mmm) cc_final: 0.6233 (mmm) REVERT: A 808 MET cc_start: 0.8290 (tmm) cc_final: 0.7361 (ttp) REVERT: A 875 MET cc_start: 0.8013 (tmm) cc_final: 0.7305 (mtm) REVERT: A 902 HIS cc_start: 0.8251 (p90) cc_final: 0.7514 (p-80) REVERT: A 952 ASP cc_start: 0.8740 (t0) cc_final: 0.8481 (p0) REVERT: A 994 LEU cc_start: 0.8969 (tp) cc_final: 0.8633 (tp) REVERT: A 1010 ASP cc_start: 0.8492 (m-30) cc_final: 0.7933 (p0) REVERT: B 158 LEU cc_start: 0.9003 (mt) cc_final: 0.8551 (tp) REVERT: B 197 PHE cc_start: 0.8194 (m-10) cc_final: 0.7862 (m-80) REVERT: B 274 MET cc_start: 0.8331 (mmm) cc_final: 0.7812 (mmm) REVERT: B 599 PHE cc_start: 0.9202 (m-80) cc_final: 0.8817 (m-80) REVERT: B 770 MET cc_start: 0.6589 (tmm) cc_final: 0.6221 (tmm) REVERT: B 808 MET cc_start: 0.6832 (mtm) cc_final: 0.5826 (mpp) REVERT: B 994 LEU cc_start: 0.8734 (mt) cc_final: 0.8471 (mt) REVERT: B 1002 LEU cc_start: 0.9093 (tp) cc_final: 0.8126 (tp) REVERT: B 1005 TRP cc_start: 0.8120 (m100) cc_final: 0.7221 (m100) REVERT: C 106 LYS cc_start: 0.9510 (mttt) cc_final: 0.9031 (tttt) REVERT: C 184 MET cc_start: 0.8698 (ttm) cc_final: 0.8314 (tpp) REVERT: C 401 VAL cc_start: 0.9541 (t) cc_final: 0.9326 (t) REVERT: C 487 TYR cc_start: 0.8620 (m-80) cc_final: 0.7996 (m-80) REVERT: C 597 ASP cc_start: 0.9083 (m-30) cc_final: 0.8810 (m-30) REVERT: C 765 LEU cc_start: 0.7935 (tp) cc_final: 0.7501 (tp) REVERT: C 775 MET cc_start: 0.8362 (ppp) cc_final: 0.8021 (ppp) REVERT: C 792 LYS cc_start: 0.7754 (mttt) cc_final: 0.7277 (ttpt) REVERT: C 875 MET cc_start: 0.8024 (pmm) cc_final: 0.7670 (pmm) REVERT: C 970 PHE cc_start: 0.9491 (p90) cc_final: 0.9218 (p90) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.2926 time to fit residues: 134.9057 Evaluate side-chains 221 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 2.372 ------------------------------------------------------------------------------- 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: 0.5980 chunk 168 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 chunk 199 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 217 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 62 optimal weight: 0.0020 chunk 30 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS ** C 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 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 = 0.3733 r_free = 0.3733 target = 0.082249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.061425 restraints weight = 117019.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.063310 restraints weight = 71632.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.064596 restraints weight = 51241.714| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22011 Z= 0.103 Angle : 0.615 11.947 29697 Z= 0.309 Chirality : 0.040 0.184 3420 Planarity : 0.003 0.043 3765 Dihedral : 4.645 29.579 2871 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -0.03 (0.17), residues: 2700 helix: 1.47 (0.16), residues: 1197 sheet: -0.27 (0.28), residues: 318 loop : -1.55 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 888 HIS 0.007 0.001 HIS A 744 PHE 0.019 0.001 PHE A 957 TYR 0.020 0.001 TYR A 715 ARG 0.004 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.02937 ( 931) hydrogen bonds : angle 4.23324 ( 2601) covalent geometry : bond 0.00215 (22011) covalent geometry : angle 0.61544 (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 304 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 2.790 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 388 ARG cc_start: 0.9123 (mtt180) cc_final: 0.8860 (mtt90) REVERT: A 503 ARG cc_start: 0.9192 (mtp85) cc_final: 0.8979 (ttm110) REVERT: A 605 CYS cc_start: 0.8296 (m) cc_final: 0.7032 (t) REVERT: A 611 PHE cc_start: 0.8120 (m-80) cc_final: 0.7696 (m-10) REVERT: A 755 LEU cc_start: 0.9106 (pp) cc_final: 0.8769 (tt) REVERT: A 793 MET cc_start: 0.6422 (mmm) cc_final: 0.6049 (mmm) REVERT: A 826 GLN cc_start: 0.8934 (mp10) cc_final: 0.8669 (mp10) REVERT: A 875 MET cc_start: 0.8034 (tmm) cc_final: 0.6439 (mtm) REVERT: A 902 HIS cc_start: 0.8172 (p90) cc_final: 0.7392 (t-90) REVERT: A 952 ASP cc_start: 0.8706 (t0) cc_final: 0.8380 (p0) REVERT: A 994 LEU cc_start: 0.8966 (tp) cc_final: 0.8638 (tp) REVERT: A 1010 ASP cc_start: 0.8432 (m-30) cc_final: 0.7895 (p0) REVERT: B 197 PHE cc_start: 0.8150 (m-10) cc_final: 0.7777 (m-80) REVERT: B 274 MET cc_start: 0.8225 (mmm) cc_final: 0.7628 (mmm) REVERT: B 335 MET cc_start: 0.8085 (tmm) cc_final: 0.7855 (tmm) REVERT: B 599 PHE cc_start: 0.9171 (m-80) cc_final: 0.8778 (m-80) REVERT: B 770 MET cc_start: 0.6610 (tmm) cc_final: 0.6241 (tmm) REVERT: B 808 MET cc_start: 0.6868 (mtm) cc_final: 0.5862 (mpp) REVERT: B 854 ASP cc_start: 0.7271 (t0) cc_final: 0.6893 (t70) REVERT: B 994 LEU cc_start: 0.8615 (mt) cc_final: 0.8402 (mt) REVERT: B 1002 LEU cc_start: 0.9113 (tp) cc_final: 0.8142 (tp) REVERT: B 1005 TRP cc_start: 0.7917 (m100) cc_final: 0.7329 (m100) REVERT: C 106 LYS cc_start: 0.9520 (mttt) cc_final: 0.9016 (tttm) REVERT: C 184 MET cc_start: 0.8592 (ttm) cc_final: 0.8246 (tpp) REVERT: C 401 VAL cc_start: 0.9497 (t) cc_final: 0.9237 (t) REVERT: C 487 TYR cc_start: 0.8545 (m-80) cc_final: 0.7913 (m-80) REVERT: C 550 ASN cc_start: 0.9060 (m-40) cc_final: 0.8639 (m-40) REVERT: C 571 LEU cc_start: 0.9632 (mm) cc_final: 0.9417 (mt) REVERT: C 597 ASP cc_start: 0.9004 (m-30) cc_final: 0.8713 (m-30) REVERT: C 714 ILE cc_start: 0.9078 (tp) cc_final: 0.8869 (tp) REVERT: C 775 MET cc_start: 0.8209 (ppp) cc_final: 0.7980 (ppp) REVERT: C 912 LEU cc_start: 0.9309 (mp) cc_final: 0.8805 (mm) REVERT: C 969 PHE cc_start: 0.8962 (p90) cc_final: 0.8640 (p90) REVERT: C 970 PHE cc_start: 0.9481 (p90) cc_final: 0.9228 (p90) REVERT: C 999 GLU cc_start: 0.8171 (tp30) cc_final: 0.7694 (tm-30) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2917 time to fit residues: 144.2791 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 : 2.469 ------------------------------------------------------------------------------- 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: 3.9990 chunk 109 optimal weight: 0.7980 chunk 170 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.081239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.060397 restraints weight = 115522.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.062240 restraints weight = 71011.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.063483 restraints weight = 50921.505| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.6407 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= 0.119 Angle : 0.625 12.346 29697 Z= 0.319 Chirality : 0.041 0.196 3420 Planarity : 0.003 0.042 3765 Dihedral : 4.698 30.153 2871 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 0.02 (0.17), residues: 2700 helix: 1.53 (0.16), residues: 1185 sheet: -0.42 (0.28), residues: 321 loop : -1.46 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 888 HIS 0.008 0.001 HIS A 744 PHE 0.023 0.001 PHE B 957 TYR 0.018 0.001 TYR C 594 ARG 0.005 0.000 ARG B 329 Details of bonding type rmsd hydrogen bonds : bond 0.03034 ( 931) hydrogen bonds : angle 4.31317 ( 2601) covalent geometry : bond 0.00256 (22011) covalent geometry : angle 0.62529 (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 280 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 2.397 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 388 ARG cc_start: 0.9113 (mtt180) cc_final: 0.8850 (mtt90) REVERT: A 503 ARG cc_start: 0.9152 (mtp85) cc_final: 0.8598 (ttm110) REVERT: A 611 PHE cc_start: 0.8080 (m-80) cc_final: 0.7616 (m-10) REVERT: A 755 LEU cc_start: 0.9109 (pp) cc_final: 0.8794 (tt) REVERT: A 793 MET cc_start: 0.6450 (mmm) cc_final: 0.6093 (mmm) REVERT: A 875 MET cc_start: 0.8039 (tmm) cc_final: 0.7287 (mtm) REVERT: A 902 HIS cc_start: 0.8158 (p90) cc_final: 0.7361 (p90) REVERT: A 952 ASP cc_start: 0.8759 (t0) cc_final: 0.8438 (p0) REVERT: A 994 LEU cc_start: 0.8928 (tp) cc_final: 0.8625 (tp) REVERT: A 1010 ASP cc_start: 0.8490 (m-30) cc_final: 0.7935 (p0) REVERT: B 197 PHE cc_start: 0.8205 (m-10) cc_final: 0.7821 (m-80) REVERT: B 274 MET cc_start: 0.8236 (mmm) cc_final: 0.7704 (mmm) REVERT: B 562 TYR cc_start: 0.8479 (t80) cc_final: 0.8114 (t80) REVERT: B 599 PHE cc_start: 0.9165 (m-80) cc_final: 0.8798 (m-80) REVERT: B 717 LEU cc_start: 0.9513 (mm) cc_final: 0.9134 (tp) REVERT: B 770 MET cc_start: 0.6591 (tmm) cc_final: 0.6275 (tmm) REVERT: B 808 MET cc_start: 0.6911 (mtm) cc_final: 0.5902 (mpp) REVERT: B 854 ASP cc_start: 0.7262 (t0) cc_final: 0.6913 (t70) REVERT: B 1002 LEU cc_start: 0.9066 (tp) cc_final: 0.8049 (tp) REVERT: B 1005 TRP cc_start: 0.8068 (m100) cc_final: 0.7509 (m100) REVERT: C 106 LYS cc_start: 0.9533 (mttt) cc_final: 0.9031 (tttm) REVERT: C 184 MET cc_start: 0.8630 (ttm) cc_final: 0.8290 (tpp) REVERT: C 203 LEU cc_start: 0.9561 (mt) cc_final: 0.9352 (mp) REVERT: C 401 VAL cc_start: 0.9539 (t) cc_final: 0.9292 (t) REVERT: C 487 TYR cc_start: 0.8575 (m-80) cc_final: 0.7927 (m-80) REVERT: C 550 ASN cc_start: 0.9079 (m-40) cc_final: 0.8636 (m-40) REVERT: C 597 ASP cc_start: 0.8993 (m-30) cc_final: 0.8757 (m-30) REVERT: C 599 PHE cc_start: 0.9081 (m-80) cc_final: 0.8701 (m-80) REVERT: C 775 MET cc_start: 0.8207 (ppp) cc_final: 0.7930 (ppp) REVERT: C 875 MET cc_start: 0.7929 (pmm) cc_final: 0.7493 (pmm) REVERT: C 912 LEU cc_start: 0.9319 (mp) cc_final: 0.9032 (mp) REVERT: C 969 PHE cc_start: 0.8969 (p90) cc_final: 0.8619 (p90) REVERT: C 970 PHE cc_start: 0.9508 (p90) cc_final: 0.9243 (p90) REVERT: C 999 GLU cc_start: 0.8181 (tp30) cc_final: 0.7700 (tm-30) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.3031 time to fit residues: 136.6511 Evaluate side-chains 222 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 2.278 ------------------------------------------------------------------------------- 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: 0.8980 chunk 185 optimal weight: 0.0170 chunk 51 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 192 optimal weight: 0.4980 chunk 137 optimal weight: 8.9990 chunk 242 optimal weight: 9.9990 chunk 256 optimal weight: 20.0000 overall best weight: 2.2822 ------------------------------------------------------------------------------- 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 865 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 HIS ** B 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1006 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.079483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.058539 restraints weight = 121912.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.060348 restraints weight = 75174.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.061594 restraints weight = 54181.486| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.6727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22011 Z= 0.167 Angle : 0.681 13.636 29697 Z= 0.348 Chirality : 0.042 0.215 3420 Planarity : 0.004 0.050 3765 Dihedral : 5.031 30.859 2871 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 1.34 (0.16), residues: 1173 sheet: -0.32 (0.30), residues: 279 loop : -1.57 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 888 HIS 0.007 0.001 HIS A 797 PHE 0.024 0.002 PHE A 197 TYR 0.018 0.002 TYR C 367 ARG 0.008 0.001 ARG B 329 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 931) hydrogen bonds : angle 4.61217 ( 2601) covalent geometry : bond 0.00356 (22011) covalent geometry : angle 0.68054 (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 262 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 2.434 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 388 ARG cc_start: 0.9127 (mtt180) cc_final: 0.8745 (mtt-85) REVERT: A 503 ARG cc_start: 0.9181 (mtp85) cc_final: 0.8541 (ttm110) REVERT: A 579 PHE cc_start: 0.9120 (m-10) cc_final: 0.8523 (m-80) REVERT: A 611 PHE cc_start: 0.8069 (m-80) cc_final: 0.7673 (m-80) REVERT: A 718 MET cc_start: 0.8158 (ppp) cc_final: 0.7942 (ppp) REVERT: A 793 MET cc_start: 0.6414 (mmm) cc_final: 0.6047 (mmm) REVERT: A 875 MET cc_start: 0.8103 (tmm) cc_final: 0.6381 (mtm) REVERT: A 902 HIS cc_start: 0.8217 (p90) cc_final: 0.7519 (t-90) REVERT: A 952 ASP cc_start: 0.8939 (t0) cc_final: 0.8559 (p0) REVERT: A 994 LEU cc_start: 0.8897 (tp) cc_final: 0.8615 (tp) REVERT: B 158 LEU cc_start: 0.8611 (mp) cc_final: 0.7972 (tp) REVERT: B 184 MET cc_start: 0.9005 (ppp) cc_final: 0.8799 (ppp) REVERT: B 274 MET cc_start: 0.8407 (mmm) cc_final: 0.7942 (mmm) REVERT: B 562 TYR cc_start: 0.8755 (t80) cc_final: 0.8447 (t80) REVERT: B 599 PHE cc_start: 0.9211 (m-80) cc_final: 0.8950 (m-80) REVERT: B 770 MET cc_start: 0.6721 (tmm) cc_final: 0.6352 (tmm) REVERT: B 1002 LEU cc_start: 0.9027 (tp) cc_final: 0.7742 (tp) REVERT: B 1005 TRP cc_start: 0.8212 (m100) cc_final: 0.7350 (m100) REVERT: C 106 LYS cc_start: 0.9519 (mttt) cc_final: 0.9119 (mmmt) REVERT: C 317 LEU cc_start: 0.9187 (mt) cc_final: 0.8939 (mt) REVERT: C 401 VAL cc_start: 0.9570 (t) cc_final: 0.9363 (t) REVERT: C 487 TYR cc_start: 0.8643 (m-80) cc_final: 0.7931 (m-80) REVERT: C 550 ASN cc_start: 0.9084 (m-40) cc_final: 0.8649 (m110) REVERT: C 597 ASP cc_start: 0.8936 (m-30) cc_final: 0.8666 (m-30) REVERT: C 599 PHE cc_start: 0.9183 (m-80) cc_final: 0.8893 (m-80) REVERT: C 770 MET cc_start: 0.7979 (tpt) cc_final: 0.7698 (mmt) REVERT: C 775 MET cc_start: 0.8260 (ppp) cc_final: 0.7933 (ppp) REVERT: C 795 LEU cc_start: 0.8544 (mp) cc_final: 0.8280 (tp) REVERT: C 912 LEU cc_start: 0.9263 (mp) cc_final: 0.8676 (mt) REVERT: C 969 PHE cc_start: 0.9080 (p90) cc_final: 0.8867 (p90) REVERT: C 970 PHE cc_start: 0.9519 (p90) cc_final: 0.9281 (p90) REVERT: C 1019 PHE cc_start: 0.7894 (t80) cc_final: 0.7635 (t80) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.3101 time to fit residues: 130.1425 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 : 2.569 ------------------------------------------------------------------------------- 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: 0.7980 chunk 127 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 236 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 96 optimal weight: 0.0670 chunk 122 optimal weight: 10.0000 overall best weight: 0.9724 ------------------------------------------------------------------------------- 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 103 GLN B 162 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.081052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.059992 restraints weight = 117971.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.061833 restraints weight = 73053.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.063059 restraints weight = 52792.287| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.6839 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= 0.111 Angle : 0.632 12.132 29697 Z= 0.320 Chirality : 0.040 0.184 3420 Planarity : 0.004 0.131 3765 Dihedral : 4.824 30.013 2871 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.07 (0.17), residues: 2700 helix: 1.47 (0.16), residues: 1185 sheet: -0.31 (0.29), residues: 306 loop : -1.56 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 888 HIS 0.006 0.001 HIS A 797 PHE 0.018 0.001 PHE C 957 TYR 0.015 0.001 TYR A 715 ARG 0.007 0.000 ARG B 530 Details of bonding type rmsd hydrogen bonds : bond 0.03042 ( 931) hydrogen bonds : angle 4.35533 ( 2601) covalent geometry : bond 0.00240 (22011) covalent geometry : angle 0.63217 (29697) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7156.24 seconds wall clock time: 126 minutes 36.89 seconds (7596.89 seconds total)