Starting phenix.real_space_refine on Fri Mar 22 13:07:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/03_2024/3jby_6488.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/03_2024/3jby_6488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/03_2024/3jby_6488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/03_2024/3jby_6488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/03_2024/3jby_6488.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jby_6488/03_2024/3jby_6488.pdb" } resolution = 3.7 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16846 atoms to isotropic. 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 124 5.49 5 S 106 5.16 5 C 10202 2.51 5 N 2978 2.21 5 O 3430 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 513": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A GLU 741": "OE1" <-> "OE2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A ARG 795": "NH1" <-> "NH2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 999": "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 TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 731": "OE1" <-> "OE2" Residue "C ARG 795": "NH1" <-> "NH2" Residue "C ARG 848": "NH1" <-> "NH2" Residue "C ARG 870": "NH1" <-> "NH2" Residue "C ARG 971": "NH1" <-> "NH2" Residue "C ARG 999": "NH1" <-> "NH2" Residue "C GLU 1005": "OE1" <-> "OE2" 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 GLU 125": "OE1" <-> "OE2" 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 GLU 280": "OE1" <-> "OE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 315": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16846 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4435 Classifications: {'peptide': 550} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 524} 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: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4435 Classifications: {'peptide': 550} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 524} 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: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 306 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "F" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 639 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "G" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 639 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "H" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 306 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "I" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 326 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "J" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 326 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} 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 2107 SG CYS A 749 96.116 79.954 64.147 1.00 7.90 S ATOM 9256 SG CYS C 749 56.429 25.315 64.298 1.00 9.51 S Time building chain proxies: 9.47, per 1000 atoms: 0.56 Number of scatterers: 16846 At special positions: 0 Unit cell: (153.75, 107.01, 121.77, 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 124 15.00 O 3430 8.00 N 2978 7.00 C 10202 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: 7.95 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 19 sheets defined 34.6% alpha, 23.2% beta 34 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 6.04 Creating SS restraints... Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 518 through 524 Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 589 through 600 Processing helix chain 'A' and resid 686 through 707 removed outlier: 3.938A pdb=" N LEU A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Proline residue: A 696 - end of helix removed outlier: 4.564A pdb=" N GLU A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 755 through 762 removed outlier: 3.513A 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 removed outlier: 3.747A pdb=" N ASP A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 835 removed outlier: 3.510A pdb=" N CYS A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 4.112A 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 removed outlier: 3.802A pdb=" N MET A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 889 Processing helix chain 'A' and resid 894 through 917 removed outlier: 3.755A pdb=" N GLU A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 924 through 930 Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 946 through 951 removed outlier: 3.698A pdb=" N TYR A 950 " --> pdb=" O PHE A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 975 through 979 Processing helix chain 'A' and resid 980 through 996 removed outlier: 3.600A pdb=" N ASN A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1017 removed outlier: 4.616A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A1008 " --> pdb=" O PHE A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1024 removed outlier: 3.520A pdb=" N GLN A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE A1024 " --> pdb=" O TYR A1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 518 through 524 removed outlier: 3.547A pdb=" N ASN C 524 " --> pdb=" O HIS C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 529 removed outlier: 3.987A pdb=" N GLU C 528 " --> pdb=" O ALA C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 600 removed outlier: 4.995A pdb=" N GLU C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASP C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.755A 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 738 Processing helix chain 'C' and resid 757 through 762 Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 814 through 835 removed outlier: 3.512A pdb=" N CYS C 818 " --> pdb=" O ASP C 814 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 890 removed outlier: 3.681A pdb=" N ALA C 887 " --> pdb=" O GLU C 883 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 888 " --> pdb=" O ALA C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 917 Proline residue: C 913 - end of helix Processing helix chain 'C' and resid 919 through 924 Processing helix chain 'C' and resid 924 through 930 Processing helix chain 'C' and resid 930 through 946 Processing helix chain 'C' and resid 946 through 951 removed outlier: 3.522A pdb=" N TYR C 950 " --> pdb=" O PHE C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 964 Processing helix chain 'C' and resid 964 through 973 Processing helix chain 'C' and resid 980 through 993 removed outlier: 4.642A pdb=" N GLY C 986 " --> pdb=" O GLY C 982 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 987 " --> pdb=" O ASN C 983 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 4.519A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 removed outlier: 3.583A pdb=" N GLN C1022 " --> pdb=" O SER C1018 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C1024 " --> pdb=" O TYR C1020 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C1027 " --> pdb=" O LYS C1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 314 Processing sheet with id= A, first strand: chain 'A' and resid 536 through 539 removed outlier: 3.531A pdb=" N PHE A 611 " --> pdb=" O SER A 719 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 620 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE A 642 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU A 677 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 536 through 539 removed outlier: 3.531A pdb=" N PHE A 611 " --> pdb=" O SER A 719 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 620 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N MET A 647 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLN A 664 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE A 649 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 2 through 6 removed outlier: 3.819A pdb=" N PHE B 345 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 20 through 23 removed outlier: 4.568A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.787A pdb=" N SER B 61 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N CYS B 124 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 141 through 147 Processing sheet with id= G, first strand: chain 'B' and resid 159 through 161 Processing sheet with id= H, first strand: chain 'B' and resid 209 through 212 Processing sheet with id= I, first strand: chain 'B' and resid 263 through 265 Processing sheet with id= J, first strand: chain 'C' and resid 536 through 539 removed outlier: 6.574A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG C 725 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL C 615 " --> pdb=" O ARG C 725 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 536 through 539 removed outlier: 6.574A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG C 725 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL C 615 " --> pdb=" O ARG C 725 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N MET C 647 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN C 664 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE C 649 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 2 through 6 removed outlier: 3.906A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 20 through 23 removed outlier: 4.547A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 76 through 80 removed outlier: 4.490A pdb=" N LEU D 106 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 96 through 97 removed outlier: 3.773A pdb=" N GLU D 101 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 141 through 147 Processing sheet with id= Q, first strand: chain 'D' and resid 159 through 161 Processing sheet with id= R, first strand: chain 'D' and resid 209 through 212 Processing sheet with id= S, first strand: chain 'D' and resid 263 through 265 removed outlier: 4.088A pdb=" N CYS D 287 " --> pdb=" O ARG D 302 " (cutoff:3.500A) 652 hydrogen bonds defined for protein. 1815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 7.06 Time building geometry restraints manager: 8.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2888 1.32 - 1.45: 6125 1.45 - 1.59: 8094 1.59 - 1.72: 201 1.72 - 1.86: 158 Bond restraints: 17466 Sorted by residual: bond pdb=" CA PRO D 339 " pdb=" C PRO D 339 " ideal model delta sigma weight residual 1.517 1.576 -0.059 9.30e-03 1.16e+04 4.03e+01 bond pdb=" C1' DG F 15 " pdb=" N9 DG F 15 " ideal model delta sigma weight residual 1.460 1.342 0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" CA PRO B 339 " pdb=" C PRO B 339 " ideal model delta sigma weight residual 1.517 1.568 -0.051 9.30e-03 1.16e+04 2.97e+01 bond pdb=" C SER A 985 " pdb=" N GLY A 986 " ideal model delta sigma weight residual 1.333 1.402 -0.070 1.31e-02 5.83e+03 2.83e+01 bond pdb=" CA ASN C 983 " pdb=" C ASN C 983 " ideal model delta sigma weight residual 1.525 1.479 0.046 1.02e-02 9.61e+03 2.02e+01 ... (remaining 17461 not shown) Histogram of bond angle deviations from ideal: 95.29 - 103.20: 417 103.20 - 111.11: 7398 111.11 - 119.03: 7295 119.03 - 126.94: 8538 126.94 - 134.85: 488 Bond angle restraints: 24136 Sorted by residual: angle pdb=" N PRO D 339 " pdb=" CA PRO D 339 " pdb=" C PRO D 339 " ideal model delta sigma weight residual 110.70 121.88 -11.18 1.22e+00 6.72e-01 8.40e+01 angle pdb=" N ARG A 999 " pdb=" CA ARG A 999 " pdb=" C ARG A 999 " ideal model delta sigma weight residual 111.14 120.34 -9.20 1.08e+00 8.57e-01 7.26e+01 angle pdb=" C THR D 338 " pdb=" N PRO D 339 " pdb=" CA PRO D 339 " ideal model delta sigma weight residual 120.38 128.86 -8.48 1.03e+00 9.43e-01 6.77e+01 angle pdb=" N PRO B 339 " pdb=" CA PRO B 339 " pdb=" C PRO B 339 " ideal model delta sigma weight residual 110.70 120.21 -9.51 1.22e+00 6.72e-01 6.07e+01 angle pdb=" N ARG C 999 " pdb=" CA ARG C 999 " pdb=" C ARG C 999 " ideal model delta sigma weight residual 111.40 119.25 -7.85 1.22e+00 6.72e-01 4.15e+01 ... (remaining 24131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.34: 9194 29.34 - 58.68: 948 58.68 - 88.02: 46 88.02 - 117.35: 6 117.35 - 146.69: 4 Dihedral angle restraints: 10198 sinusoidal: 4986 harmonic: 5212 Sorted by residual: dihedral pdb=" CA ASP A 658 " pdb=" C ASP A 658 " pdb=" N GLY A 659 " pdb=" CA GLY A 659 " ideal model delta harmonic sigma weight residual 180.00 137.23 42.77 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CA ASP C 658 " pdb=" C ASP C 658 " pdb=" N GLY C 659 " pdb=" CA GLY C 659 " ideal model delta harmonic sigma weight residual 180.00 142.38 37.62 0 5.00e+00 4.00e-02 5.66e+01 dihedral pdb=" CA PHE A1004 " pdb=" C PHE A1004 " pdb=" N GLU A1005 " pdb=" CA GLU A1005 " ideal model delta harmonic sigma weight residual -180.00 -145.84 -34.16 0 5.00e+00 4.00e-02 4.67e+01 ... (remaining 10195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1802 0.065 - 0.129: 655 0.129 - 0.193: 152 0.193 - 0.258: 20 0.258 - 0.322: 7 Chirality restraints: 2636 Sorted by residual: chirality pdb=" CB ILE D 272 " pdb=" CA ILE D 272 " pdb=" CG1 ILE D 272 " pdb=" CG2 ILE D 272 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA THR C 493 " pdb=" N THR C 493 " pdb=" C THR C 493 " pdb=" CB THR C 493 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' DG H 7 " pdb=" C4' DG H 7 " pdb=" O3' DG H 7 " pdb=" C2' DG H 7 " both_signs ideal model delta sigma weight residual False -2.66 -2.37 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 2633 not shown) Planarity restraints: 2690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG F 1 " 0.033 2.00e-02 2.50e+03 2.58e-02 1.99e+01 pdb=" N9 DG F 1 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DG F 1 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG F 1 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG F 1 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG F 1 " -0.046 2.00e-02 2.50e+03 pdb=" O6 DG F 1 " 0.047 2.00e-02 2.50e+03 pdb=" N1 DG F 1 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DG F 1 " -0.039 2.00e-02 2.50e+03 pdb=" N2 DG F 1 " 0.026 2.00e-02 2.50e+03 pdb=" N3 DG F 1 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG F 1 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG G 1 " 0.047 2.00e-02 2.50e+03 2.53e-02 1.92e+01 pdb=" N9 DG G 1 " -0.032 2.00e-02 2.50e+03 pdb=" C8 DG G 1 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG G 1 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG G 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG G 1 " -0.033 2.00e-02 2.50e+03 pdb=" O6 DG G 1 " 0.047 2.00e-02 2.50e+03 pdb=" N1 DG G 1 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG G 1 " -0.024 2.00e-02 2.50e+03 pdb=" N2 DG G 1 " 0.020 2.00e-02 2.50e+03 pdb=" N3 DG G 1 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DG G 1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG G 15 " -0.057 2.00e-02 2.50e+03 2.23e-02 1.49e+01 pdb=" N9 DG G 15 " 0.037 2.00e-02 2.50e+03 pdb=" C8 DG G 15 " 0.020 2.00e-02 2.50e+03 pdb=" N7 DG G 15 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG G 15 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG G 15 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG G 15 " -0.026 2.00e-02 2.50e+03 pdb=" N1 DG G 15 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG G 15 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG G 15 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG G 15 " 0.013 2.00e-02 2.50e+03 pdb=" C4 DG G 15 " 0.005 2.00e-02 2.50e+03 ... (remaining 2687 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 276 2.59 - 3.17: 15173 3.17 - 3.75: 27503 3.75 - 4.32: 37786 4.32 - 4.90: 59813 Nonbonded interactions: 140551 Sorted by model distance: nonbonded pdb=" NE2 GLN A 858 " pdb=" O ALA A 887 " model vdw 2.015 2.520 nonbonded pdb=" OE2 GLU C 981 " pdb=" N2 DG F 15 " model vdw 2.100 2.520 nonbonded pdb=" OG SER C 760 " pdb=" O ASP C 951 " model vdw 2.116 2.440 nonbonded pdb=" NZ LYS A 508 " pdb=" OP1 DG F 5 " model vdw 2.133 2.520 nonbonded pdb=" O3' DA J 16 " pdb="CA CA C1103 " model vdw 2.175 2.510 ... (remaining 140546 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 2.630 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 56.230 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.015 0.129 17466 Z= 0.970 Angle : 1.574 13.709 24136 Z= 0.849 Chirality : 0.070 0.322 2636 Planarity : 0.009 0.090 2690 Dihedral : 20.891 146.691 6846 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 24.71 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.24 % Favored : 95.48 % Rotamer: Outliers : 5.74 % Allowed : 13.64 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.60 (0.15), residues: 1794 helix: -3.34 (0.14), residues: 540 sheet: -1.16 (0.26), residues: 314 loop : -2.20 (0.15), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP B 172 HIS 0.019 0.004 HIS A1028 PHE 0.029 0.005 PHE C 576 TYR 0.037 0.005 TYR A 875 ARG 0.011 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 453 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8806 (mt) REVERT: A 858 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: A 905 MET cc_start: 0.9283 (tpp) cc_final: 0.8849 (tpp) REVERT: B 186 ASP cc_start: 0.7657 (t0) cc_final: 0.7446 (t0) REVERT: B 189 PHE cc_start: 0.7109 (m-80) cc_final: 0.6524 (m-80) REVERT: B 192 CYS cc_start: 0.7887 (m) cc_final: 0.7516 (t) REVERT: B 300 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6773 (tt0) REVERT: C 515 ILE cc_start: 0.8169 (mp) cc_final: 0.7920 (mp) REVERT: C 641 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7758 (mtp180) REVERT: C 674 CYS cc_start: 0.7769 (t) cc_final: 0.7279 (p) REVERT: C 737 MET cc_start: 0.7764 (mtm) cc_final: 0.7481 (ptp) REVERT: C 778 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8401 (mtt180) REVERT: C 806 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7549 (p90) REVERT: D 186 ASP cc_start: 0.7474 (t0) cc_final: 0.6828 (m-30) REVERT: D 192 CYS cc_start: 0.7917 (m) cc_final: 0.7619 (t) outliers start: 91 outliers final: 22 residues processed: 510 average time/residue: 0.3341 time to fit residues: 242.5264 Evaluate side-chains 277 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 250 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 858 GLN Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 249 CYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 778 ARG Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 860 ARG Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain D residue 231 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 HIS ** A 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 GLN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 278 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN C 687 HIS ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 GLN C 910 GLN C 937 GLN ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17466 Z= 0.345 Angle : 0.773 8.885 24136 Z= 0.423 Chirality : 0.046 0.279 2636 Planarity : 0.006 0.079 2690 Dihedral : 22.940 155.124 3377 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.07 % Favored : 96.82 % Rotamer: Outliers : 6.19 % Allowed : 19.07 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % 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: -2.05 (0.17), residues: 1794 helix: -1.13 (0.20), residues: 564 sheet: -0.47 (0.26), residues: 326 loop : -1.84 (0.16), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 538 HIS 0.008 0.001 HIS A1013 PHE 0.017 0.002 PHE D 274 TYR 0.026 0.002 TYR A 933 ARG 0.007 0.001 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 289 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 MET cc_start: 0.8583 (ttm) cc_final: 0.8351 (tpp) REVERT: A 858 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8365 (tp40) REVERT: B 69 LEU cc_start: 0.8364 (tp) cc_final: 0.8073 (tp) REVERT: B 77 ILE cc_start: 0.8233 (mp) cc_final: 0.7994 (mt) REVERT: B 189 PHE cc_start: 0.6445 (m-80) cc_final: 0.5997 (m-80) REVERT: C 641 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7692 (mtp180) REVERT: C 705 MET cc_start: 0.7683 (mmm) cc_final: 0.7352 (mmm) REVERT: C 778 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8345 (mtt180) REVERT: C 806 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7412 (p90) REVERT: C 863 MET cc_start: 0.8230 (mmm) cc_final: 0.7663 (mmp) REVERT: D 258 ILE cc_start: 0.8562 (tp) cc_final: 0.8362 (pt) REVERT: D 317 TRP cc_start: 0.8132 (p-90) cc_final: 0.7853 (p-90) outliers start: 98 outliers final: 44 residues processed: 353 average time/residue: 0.3014 time to fit residues: 157.8911 Evaluate side-chains 272 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 225 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 858 GLN Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 657 ASP Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 778 ARG Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 ASN ** A 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 269 HIS C 524 ASN C 629 HIS ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17466 Z= 0.298 Angle : 0.704 9.097 24136 Z= 0.384 Chirality : 0.044 0.284 2636 Planarity : 0.005 0.069 2690 Dihedral : 22.708 159.242 3351 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.46 % Favored : 96.32 % Rotamer: Outliers : 5.74 % Allowed : 21.15 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % 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: -1.21 (0.18), residues: 1794 helix: 0.04 (0.21), residues: 554 sheet: -0.09 (0.27), residues: 324 loop : -1.62 (0.17), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 538 HIS 0.009 0.001 HIS D 253 PHE 0.020 0.002 PHE D 80 TYR 0.022 0.002 TYR C 933 ARG 0.009 0.001 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 249 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 MET cc_start: 0.8629 (ttm) cc_final: 0.8373 (tpp) REVERT: A 736 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7865 (mt-10) REVERT: A 799 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7749 (mmtp) REVERT: A 858 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8388 (tp40) REVERT: B 77 ILE cc_start: 0.8241 (mp) cc_final: 0.8018 (mt) REVERT: B 119 LYS cc_start: 0.8008 (ttmt) cc_final: 0.7790 (ttmm) REVERT: B 186 ASP cc_start: 0.7342 (t0) cc_final: 0.7141 (t0) REVERT: B 292 LEU cc_start: 0.6626 (pt) cc_final: 0.6135 (pp) REVERT: B 328 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8248 (tp) REVERT: C 590 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6954 (tm-30) REVERT: C 641 ARG cc_start: 0.7791 (ttp80) cc_final: 0.7589 (mtp180) REVERT: C 806 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7542 (p90) REVERT: C 863 MET cc_start: 0.8064 (mmm) cc_final: 0.7684 (mmp) REVERT: D 77 ILE cc_start: 0.8306 (mp) cc_final: 0.7988 (mt) outliers start: 91 outliers final: 52 residues processed: 307 average time/residue: 0.2808 time to fit residues: 130.3407 Evaluate side-chains 269 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 212 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 858 GLN Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 590 GLU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 GLN D 33 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17466 Z= 0.241 Angle : 0.661 9.335 24136 Z= 0.359 Chirality : 0.042 0.299 2636 Planarity : 0.005 0.074 2690 Dihedral : 22.585 160.800 3345 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.57 % Favored : 96.21 % Rotamer: Outliers : 4.92 % Allowed : 22.22 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.18), residues: 1794 helix: 0.49 (0.22), residues: 556 sheet: 0.01 (0.28), residues: 326 loop : -1.51 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 538 HIS 0.014 0.001 HIS D 253 PHE 0.018 0.001 PHE B 62 TYR 0.020 0.002 TYR A 933 ARG 0.004 0.000 ARG D 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 254 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.7448 (mmm) cc_final: 0.6970 (mmm) REVERT: A 733 MET cc_start: 0.8660 (ttm) cc_final: 0.8104 (tpp) REVERT: A 933 TYR cc_start: 0.7935 (t80) cc_final: 0.7650 (t80) REVERT: B 77 ILE cc_start: 0.8243 (mp) cc_final: 0.8038 (mt) REVERT: B 210 LEU cc_start: 0.7976 (mt) cc_final: 0.7776 (mp) REVERT: B 292 LEU cc_start: 0.6583 (pt) cc_final: 0.6151 (pp) REVERT: B 328 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8369 (tp) REVERT: C 526 GLU cc_start: 0.7578 (pm20) cc_final: 0.7306 (pm20) REVERT: C 590 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7188 (tm-30) REVERT: C 641 ARG cc_start: 0.7971 (ttp80) cc_final: 0.7690 (mtp180) REVERT: C 806 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7392 (p90) REVERT: C 863 MET cc_start: 0.7994 (mmm) cc_final: 0.7770 (mmt) REVERT: C 902 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8276 (mt) REVERT: D 77 ILE cc_start: 0.8320 (mp) cc_final: 0.8039 (mt) REVERT: D 140 HIS cc_start: 0.7364 (p-80) cc_final: 0.7109 (p-80) REVERT: D 210 LEU cc_start: 0.7883 (mt) cc_final: 0.7641 (mp) REVERT: D 328 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8462 (tp) outliers start: 78 outliers final: 53 residues processed: 297 average time/residue: 0.2917 time to fit residues: 130.7617 Evaluate side-chains 277 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 219 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 590 GLU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 328 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 669 ASN ** A 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 17466 Z= 0.396 Angle : 0.730 9.425 24136 Z= 0.393 Chirality : 0.045 0.289 2636 Planarity : 0.006 0.072 2690 Dihedral : 22.870 162.872 3339 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.46 % Favored : 95.21 % Rotamer: Outliers : 6.50 % Allowed : 21.84 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.18), residues: 1794 helix: 0.40 (0.22), residues: 562 sheet: -0.24 (0.27), residues: 336 loop : -1.52 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 538 HIS 0.009 0.002 HIS A1013 PHE 0.015 0.002 PHE B 62 TYR 0.023 0.003 TYR C 504 ARG 0.010 0.001 ARG A 991 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 211 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.7499 (mmm) cc_final: 0.7067 (mmm) REVERT: A 733 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8625 (tpp) REVERT: A 863 MET cc_start: 0.8399 (mmm) cc_final: 0.8025 (mmm) REVERT: A 933 TYR cc_start: 0.8079 (t80) cc_final: 0.7636 (t80) REVERT: B 69 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8090 (mm) REVERT: B 77 ILE cc_start: 0.8361 (mp) cc_final: 0.8139 (mt) REVERT: B 80 PHE cc_start: 0.8141 (t80) cc_final: 0.7937 (t80) REVERT: B 177 ASP cc_start: 0.8320 (m-30) cc_final: 0.8072 (m-30) REVERT: B 328 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8277 (tp) REVERT: C 590 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: C 641 ARG cc_start: 0.8264 (ttp80) cc_final: 0.8062 (mtp180) REVERT: C 705 MET cc_start: 0.7699 (mmm) cc_final: 0.7442 (mmm) REVERT: C 806 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7339 (p90) REVERT: C 863 MET cc_start: 0.8089 (mmm) cc_final: 0.7716 (mmt) REVERT: D 69 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8054 (mm) REVERT: D 77 ILE cc_start: 0.8394 (mp) cc_final: 0.8075 (mt) REVERT: D 328 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8405 (tp) outliers start: 103 outliers final: 64 residues processed: 283 average time/residue: 0.2753 time to fit residues: 119.0097 Evaluate side-chains 270 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 199 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 590 GLU Chi-restraints excluded: chain C residue 657 ASP Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 328 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 0.0770 chunk 165 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 152 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 15 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.0970 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 ASN A 687 HIS ** A 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN C 822 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17466 Z= 0.183 Angle : 0.647 9.104 24136 Z= 0.347 Chirality : 0.041 0.288 2636 Planarity : 0.005 0.072 2690 Dihedral : 22.409 164.260 3337 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.85 % Favored : 95.82 % Rotamer: Outliers : 3.98 % Allowed : 23.67 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.19), residues: 1794 helix: 0.91 (0.23), residues: 546 sheet: 0.04 (0.28), residues: 326 loop : -1.34 (0.18), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 538 HIS 0.004 0.001 HIS C 766 PHE 0.015 0.001 PHE B 62 TYR 0.025 0.002 TYR C 933 ARG 0.004 0.000 ARG C 897 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 237 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.7294 (mmm) cc_final: 0.6955 (mmm) REVERT: A 733 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8227 (tpp) REVERT: A 863 MET cc_start: 0.8366 (mmm) cc_final: 0.7995 (mmm) REVERT: A 933 TYR cc_start: 0.7931 (t80) cc_final: 0.7601 (t80) REVERT: B 69 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7738 (mm) REVERT: B 80 PHE cc_start: 0.8146 (t80) cc_final: 0.7884 (t80) REVERT: B 177 ASP cc_start: 0.8300 (m-30) cc_final: 0.8052 (m-30) REVERT: B 328 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8347 (tp) REVERT: C 590 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: C 594 MET cc_start: 0.8315 (mmp) cc_final: 0.8074 (mmt) REVERT: C 705 MET cc_start: 0.7639 (mmm) cc_final: 0.7358 (mmm) REVERT: C 842 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7769 (p0) REVERT: C 902 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8360 (mt) REVERT: D 69 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7675 (mm) REVERT: D 77 ILE cc_start: 0.8286 (mp) cc_final: 0.8048 (mt) outliers start: 63 outliers final: 37 residues processed: 277 average time/residue: 0.2757 time to fit residues: 117.4588 Evaluate side-chains 255 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 211 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 590 GLU Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 842 ASN Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 134 optimal weight: 0.0970 chunk 154 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 HIS ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17466 Z= 0.222 Angle : 0.649 8.781 24136 Z= 0.348 Chirality : 0.041 0.298 2636 Planarity : 0.005 0.070 2690 Dihedral : 22.408 164.932 3334 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.35 % Favored : 95.32 % Rotamer: Outliers : 3.60 % Allowed : 24.43 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.19), residues: 1794 helix: 0.98 (0.23), residues: 550 sheet: 0.11 (0.28), residues: 326 loop : -1.29 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 538 HIS 0.025 0.001 HIS A 687 PHE 0.020 0.001 PHE D 274 TYR 0.021 0.002 TYR C 933 ARG 0.004 0.000 ARG A 778 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 221 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.7419 (mmm) cc_final: 0.7012 (mmm) REVERT: A 933 TYR cc_start: 0.7981 (t80) cc_final: 0.7643 (t80) REVERT: B 69 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7777 (mm) REVERT: B 119 LYS cc_start: 0.7720 (ttmt) cc_final: 0.7482 (ttmt) REVERT: B 177 ASP cc_start: 0.8283 (m-30) cc_final: 0.8073 (m-30) REVERT: B 328 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8367 (tp) REVERT: C 590 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: C 594 MET cc_start: 0.8344 (mmp) cc_final: 0.8118 (mmt) REVERT: C 737 MET cc_start: 0.7291 (mtp) cc_final: 0.7015 (ttm) REVERT: C 842 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.7791 (p0) REVERT: D 69 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7807 (mm) outliers start: 57 outliers final: 38 residues processed: 258 average time/residue: 0.2682 time to fit residues: 106.5277 Evaluate side-chains 248 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 205 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 590 GLU Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 842 ASN Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 166 optimal weight: 20.0000 chunk 175 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17466 Z= 0.196 Angle : 0.643 11.212 24136 Z= 0.343 Chirality : 0.040 0.289 2636 Planarity : 0.005 0.071 2690 Dihedral : 22.278 165.899 3334 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.46 % Favored : 95.26 % Rotamer: Outliers : 3.47 % Allowed : 24.68 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.19), residues: 1794 helix: 1.09 (0.23), residues: 550 sheet: 0.20 (0.28), residues: 330 loop : -1.27 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 538 HIS 0.007 0.001 HIS D 253 PHE 0.020 0.001 PHE B 80 TYR 0.020 0.002 TYR C 933 ARG 0.004 0.000 ARG C 897 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 231 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.7351 (mmm) cc_final: 0.6981 (mmm) REVERT: A 850 ARG cc_start: 0.7938 (ttm170) cc_final: 0.7588 (ttm170) REVERT: A 933 TYR cc_start: 0.7915 (t80) cc_final: 0.7612 (t80) REVERT: B 69 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7744 (mm) REVERT: B 119 LYS cc_start: 0.7681 (ttmt) cc_final: 0.7433 (ttmt) REVERT: B 210 LEU cc_start: 0.8062 (mt) cc_final: 0.7733 (mp) REVERT: C 590 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: C 594 MET cc_start: 0.8372 (mmp) cc_final: 0.8166 (mmt) REVERT: C 709 LEU cc_start: 0.8417 (tp) cc_final: 0.8207 (tp) REVERT: C 737 MET cc_start: 0.7280 (mtp) cc_final: 0.6564 (ttm) REVERT: C 842 ASN cc_start: 0.8121 (OUTLIER) cc_final: 0.7598 (p0) REVERT: D 69 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7788 (mm) REVERT: D 80 PHE cc_start: 0.8434 (t80) cc_final: 0.8180 (t80) REVERT: D 280 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8125 (tm-30) outliers start: 55 outliers final: 41 residues processed: 266 average time/residue: 0.2695 time to fit residues: 109.8542 Evaluate side-chains 257 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 212 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 590 GLU Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 842 ASN Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 175 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 154 optimal weight: 8.9990 chunk 161 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17466 Z= 0.310 Angle : 0.693 11.758 24136 Z= 0.370 Chirality : 0.042 0.163 2636 Planarity : 0.005 0.070 2690 Dihedral : 22.405 166.417 3334 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.02 % Favored : 94.65 % Rotamer: Outliers : 3.35 % Allowed : 24.81 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.19), residues: 1794 helix: 1.07 (0.23), residues: 546 sheet: 0.04 (0.27), residues: 336 loop : -1.25 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 538 HIS 0.007 0.001 HIS D 253 PHE 0.019 0.002 PHE B 80 TYR 0.019 0.002 TYR C 504 ARG 0.004 0.000 ARG D 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 211 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.7504 (mmm) cc_final: 0.7083 (mmm) REVERT: A 863 MET cc_start: 0.7982 (mmm) cc_final: 0.7704 (mtp) REVERT: A 933 TYR cc_start: 0.7963 (t80) cc_final: 0.7516 (t80) REVERT: B 69 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7824 (mm) REVERT: B 119 LYS cc_start: 0.7930 (ttmt) cc_final: 0.7687 (ttmt) REVERT: C 590 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: C 705 MET cc_start: 0.7693 (mmm) cc_final: 0.7300 (mmm) REVERT: C 737 MET cc_start: 0.7646 (mtp) cc_final: 0.7014 (ttm) REVERT: D 33 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7993 (pt0) REVERT: D 69 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8006 (mm) REVERT: D 280 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8168 (tm-30) outliers start: 53 outliers final: 44 residues processed: 247 average time/residue: 0.2716 time to fit residues: 103.1540 Evaluate side-chains 255 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 207 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 590 GLU Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 1025 MET Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 116 optimal weight: 0.0470 chunk 92 optimal weight: 0.9990 chunk 119 optimal weight: 0.0980 chunk 160 optimal weight: 10.0000 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17466 Z= 0.185 Angle : 0.662 10.326 24136 Z= 0.351 Chirality : 0.040 0.185 2636 Planarity : 0.005 0.070 2690 Dihedral : 22.103 167.221 3334 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.46 % Favored : 95.26 % Rotamer: Outliers : 2.59 % Allowed : 25.95 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 1794 helix: 1.19 (0.23), residues: 544 sheet: 0.34 (0.28), residues: 336 loop : -1.28 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 538 HIS 0.006 0.001 HIS D 253 PHE 0.020 0.001 PHE B 80 TYR 0.019 0.002 TYR C 933 ARG 0.003 0.000 ARG D 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 242 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.7546 (mmm) cc_final: 0.7248 (mmm) REVERT: A 733 MET cc_start: 0.8593 (ttm) cc_final: 0.8373 (tpp) REVERT: B 69 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7617 (mm) REVERT: B 210 LEU cc_start: 0.8036 (mt) cc_final: 0.7686 (mp) REVERT: C 590 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: C 594 MET cc_start: 0.8390 (mmp) cc_final: 0.8117 (mmt) REVERT: C 705 MET cc_start: 0.7641 (mmm) cc_final: 0.7225 (mmm) REVERT: D 69 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7763 (mm) REVERT: D 77 ILE cc_start: 0.8456 (mp) cc_final: 0.8154 (mt) REVERT: D 280 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8084 (tm-30) outliers start: 41 outliers final: 33 residues processed: 266 average time/residue: 0.2670 time to fit residues: 110.5388 Evaluate side-chains 254 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 218 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 590 GLU Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.0270 chunk 138 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 8 optimal weight: 0.0000 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.120499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.096110 restraints weight = 33229.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.098867 restraints weight = 17769.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.100674 restraints weight = 12049.862| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17466 Z= 0.204 Angle : 0.673 15.614 24136 Z= 0.354 Chirality : 0.041 0.196 2636 Planarity : 0.005 0.070 2690 Dihedral : 22.092 167.579 3334 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.35 % Favored : 95.37 % Rotamer: Outliers : 2.65 % Allowed : 26.07 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.19), residues: 1794 helix: 1.14 (0.23), residues: 548 sheet: 0.41 (0.28), residues: 336 loop : -1.27 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 538 HIS 0.005 0.001 HIS B 140 PHE 0.021 0.001 PHE B 80 TYR 0.027 0.002 TYR A 933 ARG 0.003 0.000 ARG A 778 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3252.66 seconds wall clock time: 59 minutes 46.96 seconds (3586.96 seconds total)