Starting phenix.real_space_refine on Sat Feb 17 01:16:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbr_7848/02_2024/6dbr_7848_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbr_7848/02_2024/6dbr_7848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbr_7848/02_2024/6dbr_7848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbr_7848/02_2024/6dbr_7848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbr_7848/02_2024/6dbr_7848_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbr_7848/02_2024/6dbr_7848_neut.pdb" } resolution = 4.0 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= -0.000 sd= 0.009 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 2 6.06 5 P 136 5.49 5 S 106 5.16 5 C 10290 2.51 5 N 3011 2.21 5 O 3491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 490": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A ARG 795": "NH1" <-> "NH2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C ARG 513": "NH1" <-> "NH2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 731": "OE1" <-> "OE2" Residue "C ARG 795": "NH1" <-> "NH2" Residue "C ARG 848": "NH1" <-> "NH2" Residue "C ARG 849": "NH1" <-> "NH2" Residue "C ARG 870": "NH1" <-> "NH2" Residue "C ARG 971": "NH1" <-> "NH2" Residue "C ARG 999": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 315": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17040 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4437 Classifications: {'peptide': 550} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 526} Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "C" Number of atoms: 4381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4381 Classifications: {'peptide': 542} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 517} Chain breaks: 1 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "E" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 696 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "F" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "G" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 694 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "H" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 700 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2118 SG CYS A 749 58.000 80.244 22.558 1.00 57.87 S ATOM 2139 SG CYS A 752 55.870 81.445 19.736 1.00 76.36 S ATOM 9204 SG CYS C 749 62.134 58.237 102.464 1.00 61.27 S ATOM 9225 SG CYS C 752 60.643 58.094 105.519 1.00 59.68 S Time building chain proxies: 8.98, per 1000 atoms: 0.53 Number of scatterers: 17040 At special positions: 0 Unit cell: (129.99, 146.084, 123.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 4 19.99 S 106 16.00 P 136 15.00 O 3491 8.00 N 3011 7.00 C 10290 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 - 3.50 Amino acid : False - 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: 7.41 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 752 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 752 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " Number of angles added : 4 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3340 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 18 sheets defined 33.9% alpha, 23.0% beta 62 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 6.88 Creating SS restraints... Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.591A pdb=" N SER A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 527 removed outlier: 3.595A pdb=" N LYS A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 601 removed outlier: 4.625A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASP A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 686 through 704 Proline residue: A 696 - end of helix Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 755 through 762 removed outlier: 3.858A pdb=" N ASN A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 799 Processing helix chain 'A' and resid 819 through 835 removed outlier: 3.543A pdb=" N GLY A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 862 Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 881 through 889 Processing helix chain 'A' and resid 894 through 912 Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.736A pdb=" N ARG A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 917 " --> pdb=" O PRO A 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 912 through 917' Processing helix chain 'A' and resid 924 through 946 removed outlier: 3.684A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N TYR A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.533A pdb=" N HIS A 959 " --> pdb=" O THR A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 975 through 979 removed outlier: 3.594A pdb=" N ALA A 979 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 5.039A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1017 Processing helix chain 'A' and resid 1018 through 1024 Processing helix chain 'B' and resid 308 through 314 removed outlier: 3.525A pdb=" N SER B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 492 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 518 through 526 removed outlier: 3.637A pdb=" N LEU C 522 " --> pdb=" O PRO C 518 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN C 524 " --> pdb=" O HIS C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 600 removed outlier: 5.245A pdb=" N GLU C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.620A pdb=" N SER C 673 " --> pdb=" O SER C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.539A pdb=" N LEU C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) Proline residue: C 696 - end of helix Processing helix chain 'C' and resid 730 through 737 Processing helix chain 'C' and resid 757 through 762 removed outlier: 3.988A pdb=" N GLN C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 757 through 762' Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 799 Processing helix chain 'C' and resid 815 through 835 removed outlier: 3.948A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 removed outlier: 3.512A pdb=" N ARG C 848 " --> pdb=" O SER C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 881 removed outlier: 3.751A pdb=" N THR C 881 " --> pdb=" O ARG C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 889 removed outlier: 3.801A pdb=" N VAL C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 892 No H-bonds generated for 'chain 'C' and resid 890 through 892' Processing helix chain 'C' and resid 894 through 912 Processing helix chain 'C' and resid 912 through 917 removed outlier: 3.608A pdb=" N ARG C 916 " --> pdb=" O LYS C 912 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C 917 " --> pdb=" O PRO C 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 912 through 917' Processing helix chain 'C' and resid 919 through 924 Processing helix chain 'C' and resid 924 through 930 removed outlier: 3.895A pdb=" N LEU C 928 " --> pdb=" O CYS C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 946 Processing helix chain 'C' and resid 955 through 964 Processing helix chain 'C' and resid 964 through 972 Processing helix chain 'C' and resid 980 through 985 Processing helix chain 'C' and resid 987 through 996 removed outlier: 3.634A pdb=" N ARG C 994 " --> pdb=" O PHE C 990 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS C 995 " --> pdb=" O ARG C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1016 removed outlier: 3.835A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 Processing helix chain 'D' and resid 308 through 314 removed outlier: 3.709A pdb=" N SER D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 539 removed outlier: 4.031A pdb=" N PHE A 611 " --> pdb=" O SER A 719 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU A 617 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 648 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE A 642 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU A 677 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 539 removed outlier: 4.031A pdb=" N PHE A 611 " --> pdb=" O SER A 719 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU A 617 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 648 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE A 651 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR A 661 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 5.703A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 23 removed outlier: 4.254A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.774A pdb=" N SER B 61 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS B 124 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS B 89 " --> pdb=" O PHE B 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AB1, first strand: chain 'C' and resid 536 through 539 removed outlier: 3.696A pdb=" N ARG C 708 " --> pdb=" O GLN C 539 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C 611 " --> pdb=" O SER C 719 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR C 727 " --> pdb=" O GLU C 617 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N CYS C 619 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER C 648 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS C 616 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE C 646 " --> pdb=" O LYS C 616 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER C 618 " --> pdb=" O PHE C 644 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE C 644 " --> pdb=" O SER C 618 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASP C 620 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE C 642 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N MET C 622 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL C 640 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 536 through 539 removed outlier: 3.696A pdb=" N ARG C 708 " --> pdb=" O GLN C 539 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C 611 " --> pdb=" O SER C 719 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR C 727 " --> pdb=" O GLU C 617 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N CYS C 619 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER C 648 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS C 616 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE C 646 " --> pdb=" O LYS C 616 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER C 618 " --> pdb=" O PHE C 644 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE C 644 " --> pdb=" O SER C 618 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASP C 620 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE C 642 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N MET C 622 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL C 640 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N MET C 647 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLN C 664 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE C 649 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 20 through 23 removed outlier: 4.414A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N LEU D 55 " --> pdb=" O PRO D 5 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ALA D 8 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N TYR D 343 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE D 318 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 61 through 62 removed outlier: 6.706A pdb=" N SER D 61 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N CYS D 124 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 96 through 97 removed outlier: 3.926A pdb=" N GLU D 101 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AB7, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB8, first strand: chain 'D' and resid 210 through 211 Processing sheet with id=AB9, first strand: chain 'D' and resid 263 through 265 627 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 156 hydrogen bonds 308 hydrogen bond angles 0 basepair planarities 62 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 7.64 Time building geometry restraints manager: 7.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2491 1.27 - 1.40: 4716 1.40 - 1.54: 9938 1.54 - 1.68: 387 1.68 - 1.81: 158 Bond restraints: 17690 Sorted by residual: bond pdb=" CG ASN A 983 " pdb=" OD1 ASN A 983 " ideal model delta sigma weight residual 1.231 1.133 0.098 1.90e-02 2.77e+03 2.69e+01 bond pdb=" CG ASN C 524 " pdb=" OD1 ASN C 524 " ideal model delta sigma weight residual 1.231 1.142 0.089 1.90e-02 2.77e+03 2.21e+01 bond pdb=" CG ASN C 956 " pdb=" ND2 ASN C 956 " ideal model delta sigma weight residual 1.328 1.425 -0.097 2.10e-02 2.27e+03 2.14e+01 bond pdb=" CD GLN D 33 " pdb=" OE1 GLN D 33 " ideal model delta sigma weight residual 1.231 1.146 0.085 1.90e-02 2.77e+03 2.01e+01 bond pdb=" CA ALA A1027 " pdb=" C ALA A1027 " ideal model delta sigma weight residual 1.523 1.589 -0.067 1.49e-02 4.50e+03 2.00e+01 ... (remaining 17685 not shown) Histogram of bond angle deviations from ideal: 75.42 - 95.77: 4 95.77 - 116.11: 12579 116.11 - 136.45: 11910 136.45 - 156.79: 2 156.79 - 177.13: 2 Bond angle restraints: 24497 Sorted by residual: angle pdb=" CB ASN C 524 " pdb=" CG ASN C 524 " pdb=" OD1 ASN C 524 " ideal model delta sigma weight residual 120.80 177.13 -56.33 2.00e+00 2.50e-01 7.93e+02 angle pdb=" CB ASN C 956 " pdb=" CG ASN C 956 " pdb=" ND2 ASN C 956 " ideal model delta sigma weight residual 116.40 75.42 40.98 1.50e+00 4.44e-01 7.46e+02 angle pdb=" CB ASN C 524 " pdb=" CG ASN C 524 " pdb=" ND2 ASN C 524 " ideal model delta sigma weight residual 116.40 76.96 39.44 1.50e+00 4.44e-01 6.91e+02 angle pdb=" OD1 ASN C 956 " pdb=" CG ASN C 956 " pdb=" ND2 ASN C 956 " ideal model delta sigma weight residual 122.60 97.64 24.96 1.00e+00 1.00e+00 6.23e+02 angle pdb=" CB ASN C 956 " pdb=" CG ASN C 956 " pdb=" OD1 ASN C 956 " ideal model delta sigma weight residual 120.80 165.20 -44.40 2.00e+00 2.50e-01 4.93e+02 ... (remaining 24492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 9447 35.52 - 71.04: 831 71.04 - 106.57: 20 106.57 - 142.09: 0 142.09 - 177.61: 2 Dihedral angle restraints: 10300 sinusoidal: 5109 harmonic: 5191 Sorted by residual: dihedral pdb=" N HIS A1028 " pdb=" C HIS A1028 " pdb=" CA HIS A1028 " pdb=" CB HIS A1028 " ideal model delta harmonic sigma weight residual 122.80 97.75 25.05 0 2.50e+00 1.60e-01 1.00e+02 dihedral pdb=" N ASN A 983 " pdb=" C ASN A 983 " pdb=" CA ASN A 983 " pdb=" CB ASN A 983 " ideal model delta harmonic sigma weight residual 122.80 140.40 -17.60 0 2.50e+00 1.60e-01 4.96e+01 dihedral pdb=" CA ARG C 523 " pdb=" C ARG C 523 " pdb=" N ASN C 524 " pdb=" CA ASN C 524 " ideal model delta harmonic sigma weight residual 180.00 149.16 30.84 0 5.00e+00 4.00e-02 3.80e+01 ... (remaining 10297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2556 0.096 - 0.193: 113 0.193 - 0.289: 4 0.289 - 0.386: 3 0.386 - 0.482: 2 Chirality restraints: 2678 Sorted by residual: chirality pdb=" CG LEU C 751 " pdb=" CB LEU C 751 " pdb=" CD1 LEU C 751 " pdb=" CD2 LEU C 751 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CA ASN A 983 " pdb=" N ASN A 983 " pdb=" C ASN A 983 " pdb=" CB ASN A 983 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CB VAL A 713 " pdb=" CA VAL A 713 " pdb=" CG1 VAL A 713 " pdb=" CG2 VAL A 713 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.37 2.00e-01 2.50e+01 3.52e+00 ... (remaining 2675 not shown) Planarity restraints: 2691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 983 " -0.098 2.00e-02 2.50e+03 1.97e-01 3.87e+02 pdb=" CG ASN A 983 " 0.337 2.00e-02 2.50e+03 pdb=" OD1 ASN A 983 " -0.158 2.00e-02 2.50e+03 pdb=" ND2 ASN A 983 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 539 " 0.078 2.00e-02 2.50e+03 1.71e-01 2.92e+02 pdb=" CD GLN A 539 " -0.295 2.00e-02 2.50e+03 pdb=" OE1 GLN A 539 " 0.125 2.00e-02 2.50e+03 pdb=" NE2 GLN A 539 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A1028 " -0.032 2.00e-02 2.50e+03 1.29e-01 2.49e+02 pdb=" CG HIS A1028 " 0.194 2.00e-02 2.50e+03 pdb=" ND1 HIS A1028 " -0.186 2.00e-02 2.50e+03 pdb=" CD2 HIS A1028 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 HIS A1028 " 0.140 2.00e-02 2.50e+03 pdb=" NE2 HIS A1028 " -0.068 2.00e-02 2.50e+03 ... (remaining 2688 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 13 2.08 - 2.79: 4008 2.79 - 3.49: 24330 3.49 - 4.20: 41850 4.20 - 4.90: 67723 Nonbonded interactions: 137924 Sorted by model distance: nonbonded pdb=" NH2 ARG D 232 " pdb=" CG1 ILE D 234 " model vdw 1.376 3.520 nonbonded pdb=" OE2 GLU C 774 " pdb=" NH1 ARG C 778 " model vdw 1.811 2.520 nonbonded pdb=" OD2 ASP C 566 " pdb=" OH TYR D 138 " model vdw 1.905 2.440 nonbonded pdb=" OG1 THR B 97 " pdb=" OE2 GLU B 101 " model vdw 1.929 2.440 nonbonded pdb=" NZ LYS A 628 " pdb=" OP1 DT F 17 " model vdw 1.939 2.520 ... (remaining 137919 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 480 through 626 or resid 635 through 1028 or resid 1101 th \ rough 1103)) selection = (chain 'C' and (resid 480 through 1028 or resid 1101 through 1103)) } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.430 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 55.480 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 : 0.005 0.098 17690 Z= 0.312 Angle : 1.046 56.334 24497 Z= 0.644 Chirality : 0.047 0.482 2678 Planarity : 0.008 0.197 2691 Dihedral : 21.294 177.612 6960 Min Nonbonded Distance : 1.376 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.90 % Favored : 91.98 % Rotamer: Outliers : 0.25 % Allowed : 22.36 % Favored : 77.39 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.14 (0.16), residues: 1784 helix: -2.26 (0.17), residues: 561 sheet: -2.44 (0.25), residues: 330 loop : -3.23 (0.16), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 538 HIS 0.201 0.004 HIS A1028 PHE 0.018 0.002 PHE A1024 TYR 0.014 0.002 TYR C 948 ARG 0.023 0.001 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 388 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 MET cc_start: 0.7701 (mtt) cc_final: 0.7363 (mtm) REVERT: A 871 MET cc_start: 0.8035 (mpp) cc_final: 0.7789 (mmt) REVERT: A 886 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8576 (tm-30) REVERT: A 987 ASN cc_start: 0.8316 (m-40) cc_final: 0.7902 (m-40) REVERT: A 1007 GLU cc_start: 0.9265 (tt0) cc_final: 0.9045 (tm-30) REVERT: B 127 LYS cc_start: 0.9134 (tptp) cc_final: 0.8640 (tptt) REVERT: B 189 PHE cc_start: 0.8805 (m-80) cc_final: 0.8605 (m-80) REVERT: C 832 ASP cc_start: 0.8804 (m-30) cc_final: 0.8399 (m-30) REVERT: C 850 ARG cc_start: 0.9132 (ttm-80) cc_final: 0.8582 (ptm160) REVERT: D 65 ASN cc_start: 0.8435 (p0) cc_final: 0.7736 (p0) REVERT: D 200 LEU cc_start: 0.8816 (mp) cc_final: 0.8596 (mm) REVERT: D 285 MET cc_start: 0.6822 (mmt) cc_final: 0.6550 (mmt) outliers start: 4 outliers final: 2 residues processed: 390 average time/residue: 0.3473 time to fit residues: 191.5877 Evaluate side-chains 199 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 996 MET Chi-restraints excluded: chain C residue 824 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 80 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 77 optimal weight: 0.0170 chunk 149 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN C 499 GLN C 524 ASN C 539 GLN C 544 ASN C 687 HIS C 762 ASN C 766 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 GLN D 33 GLN D 222 HIS D 253 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17690 Z= 0.198 Angle : 0.677 8.434 24497 Z= 0.368 Chirality : 0.043 0.213 2678 Planarity : 0.005 0.062 2691 Dihedral : 24.026 174.538 3461 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.06 % Rotamer: Outliers : 6.27 % Allowed : 21.09 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % 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: -2.79 (0.18), residues: 1784 helix: -0.79 (0.21), residues: 556 sheet: -1.88 (0.26), residues: 326 loop : -2.56 (0.18), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 538 HIS 0.007 0.001 HIS A1028 PHE 0.017 0.001 PHE C 938 TYR 0.025 0.002 TYR B 268 ARG 0.007 0.001 ARG A 598 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 237 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 704 MET cc_start: 0.8555 (ttp) cc_final: 0.8277 (ttm) REVERT: A 871 MET cc_start: 0.8132 (mpp) cc_final: 0.7879 (mmt) REVERT: A 886 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8620 (tm-30) REVERT: A 902 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8941 (mt) REVERT: B 123 ARG cc_start: 0.8325 (ptm160) cc_final: 0.8100 (ttp80) REVERT: B 252 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.8000 (tp) REVERT: C 819 ASP cc_start: 0.8762 (t0) cc_final: 0.8491 (t0) REVERT: C 825 GLU cc_start: 0.8403 (tp30) cc_final: 0.8017 (tp30) REVERT: C 850 ARG cc_start: 0.9051 (ttm-80) cc_final: 0.8617 (ptm160) REVERT: D 64 ASN cc_start: 0.8597 (m-40) cc_final: 0.8184 (t0) REVERT: D 65 ASN cc_start: 0.8428 (p0) cc_final: 0.7970 (p0) REVERT: D 150 LYS cc_start: 0.7541 (pttm) cc_final: 0.7324 (mppt) REVERT: D 212 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7496 (ttt-90) REVERT: D 232 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7843 (pmt-80) outliers start: 99 outliers final: 36 residues processed: 320 average time/residue: 0.2763 time to fit residues: 135.8063 Evaluate side-chains 234 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 194 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 926 ASP Chi-restraints excluded: chain C residue 956 ASN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 148 ARG Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 139 optimal weight: 0.6980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 ASN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17690 Z= 0.197 Angle : 0.644 9.533 24497 Z= 0.351 Chirality : 0.042 0.202 2678 Planarity : 0.004 0.059 2691 Dihedral : 23.835 172.712 3457 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.66 % Favored : 94.28 % Rotamer: Outliers : 5.07 % Allowed : 22.61 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % 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: -2.20 (0.19), residues: 1784 helix: -0.26 (0.21), residues: 546 sheet: -1.47 (0.28), residues: 315 loop : -2.25 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 538 HIS 0.004 0.001 HIS C 687 PHE 0.018 0.001 PHE B 274 TYR 0.018 0.001 TYR C 933 ARG 0.005 0.000 ARG A 882 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 200 time to evaluate : 1.784 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: A 833 GLU cc_start: 0.9281 (tp30) cc_final: 0.8785 (pp20) REVERT: A 902 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9011 (mt) REVERT: A 905 MET cc_start: 0.9345 (mmp) cc_final: 0.8359 (tpt) REVERT: A 987 ASN cc_start: 0.8055 (m-40) cc_final: 0.7543 (m-40) REVERT: C 733 MET cc_start: 0.6811 (tpp) cc_final: 0.6583 (mpp) REVERT: C 781 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8431 (mp) REVERT: C 819 ASP cc_start: 0.8736 (t0) cc_final: 0.8464 (t0) REVERT: C 850 ARG cc_start: 0.9091 (ttm-80) cc_final: 0.8664 (ptm160) REVERT: C 905 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8225 (tmm) REVERT: C 1025 MET cc_start: 0.7853 (tpt) cc_final: 0.7624 (tpp) REVERT: D 64 ASN cc_start: 0.8812 (m-40) cc_final: 0.8300 (t0) REVERT: D 65 ASN cc_start: 0.8488 (p0) cc_final: 0.8020 (p0) REVERT: D 84 ASP cc_start: 0.8282 (m-30) cc_final: 0.7641 (p0) REVERT: D 185 ILE cc_start: 0.8946 (pt) cc_final: 0.8577 (mm) REVERT: D 212 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7521 (ttt-90) REVERT: D 232 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7941 (pmt-80) outliers start: 80 outliers final: 44 residues processed: 263 average time/residue: 0.2550 time to fit residues: 106.4639 Evaluate side-chains 222 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 173 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 773 ASP Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 926 ASP Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 116 optimal weight: 0.6980 chunk 174 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 HIS ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17690 Z= 0.289 Angle : 0.672 14.115 24497 Z= 0.363 Chirality : 0.042 0.180 2678 Planarity : 0.005 0.058 2691 Dihedral : 23.807 173.132 3457 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.22 % Favored : 93.72 % Rotamer: Outliers : 5.95 % Allowed : 23.50 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % 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: -2.20 (0.19), residues: 1784 helix: -0.30 (0.21), residues: 569 sheet: -1.49 (0.28), residues: 323 loop : -2.25 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 538 HIS 0.006 0.001 HIS D 237 PHE 0.014 0.002 PHE D 218 TYR 0.016 0.002 TYR C 933 ARG 0.004 0.000 ARG D 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 176 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8900 (t) REVERT: A 833 GLU cc_start: 0.9281 (tp30) cc_final: 0.8846 (pp20) REVERT: A 902 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9117 (mt) REVERT: A 905 MET cc_start: 0.9375 (mmp) cc_final: 0.8405 (tpt) REVERT: A 987 ASN cc_start: 0.8129 (m-40) cc_final: 0.7655 (m-40) REVERT: B 140 HIS cc_start: 0.7387 (p-80) cc_final: 0.7174 (p-80) REVERT: C 733 MET cc_start: 0.6899 (tpp) cc_final: 0.6553 (mpp) REVERT: C 781 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8509 (mp) REVERT: C 850 ARG cc_start: 0.9109 (ttm-80) cc_final: 0.8761 (ptm160) REVERT: C 869 MET cc_start: 0.7656 (mpp) cc_final: 0.7203 (mpp) REVERT: D 64 ASN cc_start: 0.9018 (m-40) cc_final: 0.8486 (t0) REVERT: D 65 ASN cc_start: 0.8682 (p0) cc_final: 0.8244 (p0) REVERT: D 185 ILE cc_start: 0.9001 (pt) cc_final: 0.8589 (mm) REVERT: D 197 LEU cc_start: 0.8757 (tp) cc_final: 0.8532 (tt) REVERT: D 212 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7668 (ttt-90) REVERT: D 224 LEU cc_start: 0.9034 (pt) cc_final: 0.8524 (tp) outliers start: 94 outliers final: 62 residues processed: 252 average time/residue: 0.2692 time to fit residues: 105.5448 Evaluate side-chains 229 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 163 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 845 ARG Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 746 THR Chi-restraints excluded: chain C residue 773 ASP Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 926 ASP Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 165 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 ASN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17690 Z= 0.181 Angle : 0.627 10.522 24497 Z= 0.337 Chirality : 0.041 0.183 2678 Planarity : 0.004 0.059 2691 Dihedral : 23.667 173.435 3457 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.66 % Favored : 94.28 % Rotamer: Outliers : 4.94 % Allowed : 24.13 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % 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: -1.80 (0.19), residues: 1784 helix: 0.24 (0.22), residues: 547 sheet: -1.42 (0.28), residues: 322 loop : -2.05 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 538 HIS 0.005 0.001 HIS D 207 PHE 0.021 0.001 PHE D 218 TYR 0.017 0.001 TYR C 933 ARG 0.004 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 188 time to evaluate : 1.815 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: A 833 GLU cc_start: 0.9274 (tp30) cc_final: 0.8747 (pp20) REVERT: A 902 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9115 (mt) REVERT: A 987 ASN cc_start: 0.7947 (m-40) cc_final: 0.7474 (m-40) REVERT: C 489 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8530 (mt) REVERT: C 605 SER cc_start: 0.7978 (OUTLIER) cc_final: 0.7471 (p) REVERT: C 606 MET cc_start: 0.7056 (ppp) cc_final: 0.6631 (ppp) REVERT: C 819 ASP cc_start: 0.8845 (t0) cc_final: 0.8615 (t0) REVERT: C 850 ARG cc_start: 0.9082 (ttm-80) cc_final: 0.8734 (ptm160) REVERT: C 869 MET cc_start: 0.7716 (mpp) cc_final: 0.7218 (mpp) REVERT: C 1025 MET cc_start: 0.7818 (tpt) cc_final: 0.7567 (tpp) REVERT: D 64 ASN cc_start: 0.8932 (m-40) cc_final: 0.8474 (t0) REVERT: D 65 ASN cc_start: 0.8634 (p0) cc_final: 0.8311 (p0) REVERT: D 212 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7641 (ttt-90) REVERT: D 224 LEU cc_start: 0.9043 (pt) cc_final: 0.8496 (tp) REVERT: D 232 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8013 (pmt-80) outliers start: 78 outliers final: 51 residues processed: 252 average time/residue: 0.2571 time to fit residues: 102.1350 Evaluate side-chains 221 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 165 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 845 ARG Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain C residue 773 ASP Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 870 ARG Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 926 ASP Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.0980 chunk 166 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 0.3980 chunk 45 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 858 GLN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17690 Z= 0.167 Angle : 0.637 11.539 24497 Z= 0.336 Chirality : 0.041 0.185 2678 Planarity : 0.004 0.066 2691 Dihedral : 23.548 173.174 3457 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.05 % Allowed : 25.21 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % 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: -1.56 (0.19), residues: 1784 helix: 0.46 (0.22), residues: 542 sheet: -1.22 (0.28), residues: 321 loop : -1.93 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 851 HIS 0.005 0.001 HIS D 207 PHE 0.015 0.001 PHE D 218 TYR 0.015 0.001 TYR C 933 ARG 0.006 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 187 time to evaluate : 1.882 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: A 506 THR cc_start: 0.7946 (m) cc_final: 0.7625 (m) REVERT: A 737 MET cc_start: 0.7614 (mmm) cc_final: 0.7343 (mtp) REVERT: A 902 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9078 (mt) REVERT: A 905 MET cc_start: 0.9260 (mmp) cc_final: 0.8265 (tpt) REVERT: A 987 ASN cc_start: 0.7989 (m-40) cc_final: 0.7727 (m-40) REVERT: B 249 CYS cc_start: 0.7898 (m) cc_final: 0.7645 (t) REVERT: B 341 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8008 (pp20) REVERT: C 605 SER cc_start: 0.7979 (OUTLIER) cc_final: 0.7488 (p) REVERT: C 733 MET cc_start: 0.6680 (tpp) cc_final: 0.6356 (mpp) REVERT: C 737 MET cc_start: 0.6722 (mtp) cc_final: 0.6327 (mtp) REVERT: C 819 ASP cc_start: 0.8762 (t0) cc_final: 0.8501 (t0) REVERT: C 831 GLN cc_start: 0.9042 (pt0) cc_final: 0.8726 (pt0) REVERT: C 850 ARG cc_start: 0.9050 (ttm-80) cc_final: 0.8705 (ptm160) REVERT: C 869 MET cc_start: 0.7834 (mpp) cc_final: 0.7397 (mpp) REVERT: C 1025 MET cc_start: 0.7885 (tpt) cc_final: 0.7605 (tpp) REVERT: D 64 ASN cc_start: 0.8839 (m-40) cc_final: 0.8380 (t0) REVERT: D 65 ASN cc_start: 0.8756 (p0) cc_final: 0.8078 (p0) REVERT: D 212 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7629 (ttt-90) REVERT: D 224 LEU cc_start: 0.9045 (pt) cc_final: 0.8451 (tp) REVERT: D 232 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8050 (pmt-80) outliers start: 64 outliers final: 47 residues processed: 239 average time/residue: 0.2795 time to fit residues: 105.1740 Evaluate side-chains 224 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 172 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 845 ARG Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain C residue 773 ASP Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 870 ARG Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 926 ASP Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 84 optimal weight: 0.0060 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17690 Z= 0.249 Angle : 0.658 10.187 24497 Z= 0.348 Chirality : 0.041 0.170 2678 Planarity : 0.004 0.065 2691 Dihedral : 23.496 172.690 3457 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.33 % Favored : 93.61 % Rotamer: Outliers : 4.43 % Allowed : 25.46 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % 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: -1.56 (0.19), residues: 1784 helix: 0.28 (0.22), residues: 562 sheet: -1.18 (0.29), residues: 321 loop : -1.86 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 538 HIS 0.006 0.001 HIS D 207 PHE 0.021 0.001 PHE D 274 TYR 0.014 0.001 TYR C 933 ARG 0.004 0.000 ARG C 897 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 165 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 622 MET cc_start: 0.8994 (tpp) cc_final: 0.8334 (mmt) REVERT: A 833 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8807 (pp20) REVERT: A 902 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9086 (mt) REVERT: A 905 MET cc_start: 0.9337 (mmp) cc_final: 0.8318 (tpt) REVERT: A 987 ASN cc_start: 0.7988 (m-40) cc_final: 0.7349 (m-40) REVERT: C 605 SER cc_start: 0.8084 (OUTLIER) cc_final: 0.7584 (p) REVERT: C 781 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8495 (mp) REVERT: C 850 ARG cc_start: 0.9065 (ttm-80) cc_final: 0.8718 (ptm160) REVERT: C 869 MET cc_start: 0.7958 (mpp) cc_final: 0.7516 (mpp) REVERT: D 64 ASN cc_start: 0.9011 (m-40) cc_final: 0.8549 (t0) REVERT: D 65 ASN cc_start: 0.8871 (p0) cc_final: 0.8425 (p0) REVERT: D 212 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7720 (ttt-90) REVERT: D 224 LEU cc_start: 0.9079 (pt) cc_final: 0.8493 (tp) outliers start: 70 outliers final: 58 residues processed: 219 average time/residue: 0.2524 time to fit residues: 89.0328 Evaluate side-chains 221 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 158 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 845 ARG Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain C residue 773 ASP Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 926 ASP Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 117 optimal weight: 0.0870 chunk 125 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 ASN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17690 Z= 0.226 Angle : 0.650 10.304 24497 Z= 0.344 Chirality : 0.041 0.172 2678 Planarity : 0.004 0.066 2691 Dihedral : 23.400 172.449 3457 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.39 % Favored : 93.55 % Rotamer: Outliers : 4.69 % Allowed : 25.52 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % 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: -1.52 (0.19), residues: 1784 helix: 0.26 (0.22), residues: 568 sheet: -1.14 (0.29), residues: 321 loop : -1.82 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 851 HIS 0.005 0.001 HIS D 207 PHE 0.019 0.001 PHE D 274 TYR 0.016 0.002 TYR A 875 ARG 0.004 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 166 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 GLU cc_start: 0.8809 (pm20) cc_final: 0.8243 (pm20) REVERT: A 622 MET cc_start: 0.8956 (tpp) cc_final: 0.8462 (mmt) REVERT: A 833 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.8815 (pp20) REVERT: A 902 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8989 (mt) REVERT: A 905 MET cc_start: 0.9273 (mmp) cc_final: 0.8299 (tpt) REVERT: A 987 ASN cc_start: 0.7961 (m-40) cc_final: 0.7208 (m-40) REVERT: B 210 LEU cc_start: 0.8528 (mt) cc_final: 0.7992 (mp) REVERT: C 567 VAL cc_start: 0.9442 (OUTLIER) cc_final: 0.9155 (t) REVERT: C 605 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.7684 (p) REVERT: C 733 MET cc_start: 0.6692 (tpp) cc_final: 0.6376 (mpp) REVERT: C 776 LEU cc_start: 0.9040 (mt) cc_final: 0.8779 (tp) REVERT: C 781 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8483 (mp) REVERT: C 831 GLN cc_start: 0.9146 (pt0) cc_final: 0.8914 (pt0) REVERT: C 869 MET cc_start: 0.8062 (mpp) cc_final: 0.7687 (mpp) REVERT: D 64 ASN cc_start: 0.9003 (m-40) cc_final: 0.8542 (t0) REVERT: D 65 ASN cc_start: 0.8915 (p0) cc_final: 0.8494 (p0) REVERT: D 77 ILE cc_start: 0.8785 (mp) cc_final: 0.8494 (mt) REVERT: D 212 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7721 (ttt-90) REVERT: D 224 LEU cc_start: 0.9091 (pt) cc_final: 0.8458 (tp) outliers start: 74 outliers final: 59 residues processed: 226 average time/residue: 0.2427 time to fit residues: 87.4707 Evaluate side-chains 221 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 156 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain C residue 773 ASP Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 870 ARG Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 926 ASP Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 324 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17690 Z= 0.233 Angle : 0.672 14.056 24497 Z= 0.351 Chirality : 0.041 0.170 2678 Planarity : 0.004 0.066 2691 Dihedral : 23.361 172.299 3457 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.73 % Favored : 93.22 % Rotamer: Outliers : 4.69 % Allowed : 26.66 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % 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: -1.50 (0.19), residues: 1784 helix: 0.26 (0.22), residues: 569 sheet: -1.13 (0.29), residues: 321 loop : -1.79 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 851 HIS 0.007 0.001 HIS C 687 PHE 0.013 0.001 PHE D 218 TYR 0.048 0.002 TYR A 875 ARG 0.025 0.000 ARG D 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 164 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 GLU cc_start: 0.8872 (pm20) cc_final: 0.8245 (pm20) REVERT: A 833 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.8825 (pp20) REVERT: A 902 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8901 (mt) REVERT: A 905 MET cc_start: 0.9279 (mmp) cc_final: 0.8313 (tpt) REVERT: A 987 ASN cc_start: 0.7905 (m-40) cc_final: 0.7489 (m-40) REVERT: B 210 LEU cc_start: 0.8579 (mt) cc_final: 0.8056 (mp) REVERT: C 605 SER cc_start: 0.8086 (OUTLIER) cc_final: 0.7586 (p) REVERT: C 733 MET cc_start: 0.6721 (tpp) cc_final: 0.6416 (mpp) REVERT: C 776 LEU cc_start: 0.8967 (mt) cc_final: 0.8721 (tp) REVERT: C 781 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8445 (mp) REVERT: C 825 GLU cc_start: 0.8111 (tp30) cc_final: 0.7890 (tp30) REVERT: C 869 MET cc_start: 0.8124 (mpp) cc_final: 0.7801 (mpp) REVERT: C 1006 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8667 (mm) REVERT: D 64 ASN cc_start: 0.9023 (m-40) cc_final: 0.8556 (t0) REVERT: D 65 ASN cc_start: 0.8945 (p0) cc_final: 0.8510 (p0) REVERT: D 73 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.7025 (mtm110) REVERT: D 77 ILE cc_start: 0.8805 (mp) cc_final: 0.8462 (mt) REVERT: D 177 ASP cc_start: 0.9107 (OUTLIER) cc_final: 0.8719 (t70) REVERT: D 212 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7741 (ttt-90) REVERT: D 224 LEU cc_start: 0.9069 (pt) cc_final: 0.8437 (tp) outliers start: 74 outliers final: 61 residues processed: 227 average time/residue: 0.2493 time to fit residues: 91.1663 Evaluate side-chains 223 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 154 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain C residue 773 ASP Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 870 ARG Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 926 ASP Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 1006 LEU Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 324 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 151 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 17690 Z= 0.263 Angle : 0.838 59.200 24497 Z= 0.467 Chirality : 0.043 0.524 2678 Planarity : 0.005 0.068 2691 Dihedral : 23.367 172.284 3457 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.61 % Favored : 93.27 % Rotamer: Outliers : 4.88 % Allowed : 26.54 % Favored : 68.59 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.50 (0.19), residues: 1784 helix: 0.27 (0.22), residues: 569 sheet: -1.12 (0.29), residues: 321 loop : -1.79 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 851 HIS 0.005 0.001 HIS D 207 PHE 0.012 0.001 PHE D 218 TYR 0.037 0.002 TYR A 875 ARG 0.017 0.000 ARG D 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 154 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 GLU cc_start: 0.8870 (pm20) cc_final: 0.8238 (pm20) REVERT: A 833 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8812 (pp20) REVERT: A 902 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8905 (mt) REVERT: A 905 MET cc_start: 0.9285 (mmp) cc_final: 0.8308 (tpt) REVERT: A 987 ASN cc_start: 0.7735 (m-40) cc_final: 0.7510 (m-40) REVERT: B 210 LEU cc_start: 0.8560 (mt) cc_final: 0.8050 (mp) REVERT: C 605 SER cc_start: 0.8088 (OUTLIER) cc_final: 0.7595 (p) REVERT: C 733 MET cc_start: 0.6735 (tpp) cc_final: 0.6325 (mpp) REVERT: C 781 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8419 (mp) REVERT: C 825 GLU cc_start: 0.8151 (tp30) cc_final: 0.7928 (tp30) REVERT: C 869 MET cc_start: 0.8123 (mpp) cc_final: 0.7804 (mpp) REVERT: C 1006 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8656 (mm) REVERT: D 64 ASN cc_start: 0.9021 (m-40) cc_final: 0.8552 (t0) REVERT: D 65 ASN cc_start: 0.8945 (p0) cc_final: 0.8504 (p0) REVERT: D 73 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6951 (mtm110) REVERT: D 77 ILE cc_start: 0.8804 (mp) cc_final: 0.8461 (mt) REVERT: D 177 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8715 (t70) REVERT: D 212 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7741 (ttt-90) REVERT: D 224 LEU cc_start: 0.9090 (pt) cc_final: 0.8450 (tp) outliers start: 77 outliers final: 64 residues processed: 219 average time/residue: 0.2473 time to fit residues: 87.5796 Evaluate side-chains 226 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 154 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain C residue 773 ASP Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 870 ARG Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 926 ASP Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 1006 LEU Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 324 LYS Chi-restraints excluded: chain D residue 331 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.089694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.066150 restraints weight = 56011.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.067946 restraints weight = 32627.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.069106 restraints weight = 23494.164| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 17690 Z= 0.263 Angle : 0.838 59.198 24497 Z= 0.467 Chirality : 0.043 0.524 2678 Planarity : 0.005 0.068 2691 Dihedral : 23.367 172.284 3457 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.61 % Favored : 93.27 % Rotamer: Outliers : 4.56 % Allowed : 26.92 % Favored : 68.52 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.50 (0.19), residues: 1784 helix: 0.27 (0.22), residues: 569 sheet: -1.12 (0.29), residues: 321 loop : -1.79 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 851 HIS 0.005 0.001 HIS D 207 PHE 0.012 0.001 PHE D 218 TYR 0.037 0.002 TYR A 875 ARG 0.017 0.000 ARG D 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3079.48 seconds wall clock time: 57 minutes 26.77 seconds (3446.77 seconds total)