Starting phenix.real_space_refine on Sun Aug 9 11:20:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kds_37144/08_2026/8kds_37144.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kds_37144/08_2026/8kds_37144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kds_37144/08_2026/8kds_37144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kds_37144/08_2026/8kds_37144.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kds_37144/08_2026/8kds_37144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kds_37144/08_2026/8kds_37144.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 165 5.16 5 C 21849 2.51 5 N 5730 2.21 5 O 6609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34353 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1630 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 10, 'TRANS': 206} Chain: "D" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "G" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1630 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 10, 'TRANS': 206} Chain: "F" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "I" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1630 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 10, 'TRANS': 206} Chain: "H" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "B" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8190 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 998} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8190 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 998} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8190 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 998} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.23, per 1000 atoms: 0.18 Number of scatterers: 34353 At special positions: 0 Unit cell: (173.74, 191.59, 208.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 165 16.00 O 6609 8.00 N 5730 7.00 C 21849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 203 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 147 " - pdb=" SG CYS I 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS H 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 389 " distance=2.03 Simple disulfide: pdb=" SG CYS B 407 " - pdb=" SG CYS B 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 552 " distance=2.03 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 515 " distance=2.03 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 617 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 676 " distance=2.03 Simple disulfide: pdb=" SG CYS B 689 " - pdb=" SG CYS B 698 " distance=2.03 Simple disulfide: pdb=" SG CYS B 761 " - pdb=" SG CYS B 783 " distance=2.03 Simple disulfide: pdb=" SG CYS B 766 " - pdb=" SG CYS B 772 " distance=2.03 Simple disulfide: pdb=" SG CYS B 863 " - pdb=" SG CYS B 874 " distance=2.03 Simple disulfide: pdb=" SG CYS B1055 " - pdb=" SG CYS B1066 " distance=2.03 Simple disulfide: pdb=" SG CYS B1105 " - pdb=" SG CYS B1149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 389 " distance=2.03 Simple disulfide: pdb=" SG CYS A 407 " - pdb=" SG CYS A 460 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 552 " distance=2.03 Simple disulfide: pdb=" SG CYS A 508 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 617 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 676 " distance=2.03 Simple disulfide: pdb=" SG CYS A 689 " - pdb=" SG CYS A 698 " distance=2.03 Simple disulfide: pdb=" SG CYS A 761 " - pdb=" SG CYS A 783 " distance=2.03 Simple disulfide: pdb=" SG CYS A 766 " - pdb=" SG CYS A 772 " distance=2.03 Simple disulfide: pdb=" SG CYS A 863 " - pdb=" SG CYS A 874 " distance=2.03 Simple disulfide: pdb=" SG CYS A1055 " - pdb=" SG CYS A1066 " distance=2.03 Simple disulfide: pdb=" SG CYS A1105 " - pdb=" SG CYS A1149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS C 200 " distance=2.03 Simple disulfide: pdb=" SG CYS C 319 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 389 " distance=2.03 Simple disulfide: pdb=" SG CYS C 407 " - pdb=" SG CYS C 460 " distance=2.03 Simple disulfide: pdb=" SG CYS C 419 " - pdb=" SG CYS C 552 " distance=2.03 Simple disulfide: pdb=" SG CYS C 508 " - pdb=" SG CYS C 515 " distance=2.03 Simple disulfide: pdb=" SG CYS C 565 " - pdb=" SG CYS C 617 " distance=2.03 Simple disulfide: pdb=" SG CYS C 644 " - pdb=" SG CYS C 676 " distance=2.03 Simple disulfide: pdb=" SG CYS C 689 " - pdb=" SG CYS C 698 " distance=2.03 Simple disulfide: pdb=" SG CYS C 761 " - pdb=" SG CYS C 783 " distance=2.03 Simple disulfide: pdb=" SG CYS C 766 " - pdb=" SG CYS C 772 " distance=2.03 Simple disulfide: pdb=" SG CYS C 863 " - pdb=" SG CYS C 874 " distance=2.03 Simple disulfide: pdb=" SG CYS C1055 " - pdb=" SG CYS C1066 " distance=2.03 Simple disulfide: pdb=" SG CYS C1105 " - pdb=" SG CYS C1149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.2 seconds 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8262 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 74 sheets defined 17.3% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 184 through 190 removed outlier: 3.511A pdb=" N HIS D 190 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 removed outlier: 3.790A pdb=" N LEU F 126 " --> pdb=" O SER F 122 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 122 through 127' Processing helix chain 'F' and resid 184 through 190 removed outlier: 3.520A pdb=" N HIS F 190 " --> pdb=" O ASP F 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 128 Processing helix chain 'H' and resid 184 through 190 Processing helix chain 'B' and resid 322 through 332 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.509A pdb=" N PHE B 370 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 removed outlier: 4.124A pdb=" N TYR B 397 " --> pdb=" O TYR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 435 No H-bonds generated for 'chain 'B' and resid 433 through 435' Processing helix chain 'B' and resid 529 through 532 Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.610A pdb=" N THR B 649 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 765 Processing helix chain 'B' and resid 769 through 777 removed outlier: 3.721A pdb=" N ALA B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 806 Processing helix chain 'B' and resid 839 through 846 Processing helix chain 'B' and resid 889 through 906 Processing helix chain 'B' and resid 909 through 914 removed outlier: 3.761A pdb=" N GLY B 912 " --> pdb=" O TRP B 909 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY B 914 " --> pdb=" O PHE B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 933 Processing helix chain 'B' and resid 935 through 942 removed outlier: 4.288A pdb=" N LEU B 939 " --> pdb=" O THR B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 963 removed outlier: 3.833A pdb=" N THR B 963 " --> pdb=" O GLU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 990 Processing helix chain 'B' and resid 1003 through 1007 removed outlier: 4.091A pdb=" N ARG B1006 " --> pdb=" O ILE B1003 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B1007 " --> pdb=" O LEU B1004 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1003 through 1007' Processing helix chain 'B' and resid 1008 through 1056 removed outlier: 3.946A pdb=" N VAL B1014 " --> pdb=" O PRO B1010 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN B1015 " --> pdb=" O GLU B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1172 removed outlier: 3.808A pdb=" N GLU B1167 " --> pdb=" O PRO B1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 removed outlier: 4.118A pdb=" N ASN A 137 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 138 " --> pdb=" O LYS A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 134 through 138' Processing helix chain 'A' and resid 191 through 195 removed outlier: 4.074A pdb=" N PHE A 194 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 195 " --> pdb=" O MET A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 191 through 195' Processing helix chain 'A' and resid 322 through 332 Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 529 through 532 Processing helix chain 'A' and resid 645 through 654 Processing helix chain 'A' and resid 760 through 765 Processing helix chain 'A' and resid 769 through 780 removed outlier: 3.912A pdb=" N ALA A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASN A 774 " --> pdb=" O THR A 770 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 806 removed outlier: 3.886A pdb=" N LEU A 786 " --> pdb=" O PHE A 782 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN A 787 " --> pdb=" O CYS A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 847 Processing helix chain 'A' and resid 889 through 906 Processing helix chain 'A' and resid 907 through 911 removed outlier: 3.706A pdb=" N THR A 910 " --> pdb=" O ALA A 907 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE A 911 " --> pdb=" O GLY A 908 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 907 through 911' Processing helix chain 'A' and resid 920 through 933 removed outlier: 3.675A pdb=" N ILE A 932 " --> pdb=" O ARG A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 942 removed outlier: 4.244A pdb=" N LEU A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 963 Processing helix chain 'A' and resid 969 through 990 Processing helix chain 'A' and resid 1002 through 1006 removed outlier: 3.541A pdb=" N ARG A1006 " --> pdb=" O ILE A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1056 removed outlier: 4.214A pdb=" N VAL A1014 " --> pdb=" O PRO A1010 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1173 removed outlier: 3.728A pdb=" N GLU A1167 " --> pdb=" O PRO A1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 312 removed outlier: 3.574A pdb=" N GLY C 311 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 332 Processing helix chain 'C' and resid 393 through 398 removed outlier: 4.139A pdb=" N TYR C 397 " --> pdb=" O TYR C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 435 No H-bonds generated for 'chain 'C' and resid 433 through 435' Processing helix chain 'C' and resid 529 through 532 Processing helix chain 'C' and resid 645 through 653 Processing helix chain 'C' and resid 760 through 765 Processing helix chain 'C' and resid 769 through 777 Processing helix chain 'C' and resid 781 through 806 Processing helix chain 'C' and resid 839 through 847 Processing helix chain 'C' and resid 889 through 906 Processing helix chain 'C' and resid 909 through 914 removed outlier: 3.725A pdb=" N GLY C 912 " --> pdb=" O TRP C 909 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY C 914 " --> pdb=" O PHE C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 933 Processing helix chain 'C' and resid 935 through 942 removed outlier: 4.170A pdb=" N LEU C 939 " --> pdb=" O THR C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 963 removed outlier: 3.838A pdb=" N THR C 963 " --> pdb=" O GLU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 990 Processing helix chain 'C' and resid 1002 through 1006 removed outlier: 3.515A pdb=" N SER C1005 " --> pdb=" O ASP C1002 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG C1006 " --> pdb=" O ILE C1003 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1002 through 1006' Processing helix chain 'C' and resid 1008 through 1056 removed outlier: 4.150A pdb=" N VAL C1014 " --> pdb=" O PRO C1010 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN C1015 " --> pdb=" O GLU C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1173 removed outlier: 3.531A pdb=" N GLU C1167 " --> pdb=" O PRO C1163 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 6 through 7 removed outlier: 4.084A pdb=" N SER E 7 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER E 77 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR E 68 " --> pdb=" O GLN E 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 35 through 39 removed outlier: 3.627A pdb=" N VAL E 96 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL E 37 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA E 91 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 149 through 150 Processing sheet with id=AA4, first strand: chain 'D' and resid 35 through 37 removed outlier: 7.185A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.832A pdb=" N ARG D 65 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR D 72 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER D 67 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 115 through 119 removed outlier: 6.311A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 155 through 156 removed outlier: 4.205A pdb=" N TRP D 149 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR D 193 " --> pdb=" O PHE D 210 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE D 210 " --> pdb=" O TYR D 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 6 through 7 removed outlier: 4.090A pdb=" N SER G 7 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER G 77 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR G 68 " --> pdb=" O GLN G 81 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 35 through 39 removed outlier: 3.571A pdb=" N VAL G 96 " --> pdb=" O HIS G 35 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL G 37 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 127 through 128 Processing sheet with id=AB2, first strand: chain 'F' and resid 35 through 37 removed outlier: 7.217A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.761A pdb=" N ARG F 65 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR F 72 " --> pdb=" O ARG F 65 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER F 67 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 115 through 119 removed outlier: 3.664A pdb=" N ASN F 138 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR F 174 " --> pdb=" O ASN F 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 155 through 156 removed outlier: 4.174A pdb=" N TRP F 149 " --> pdb=" O GLN F 156 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR F 193 " --> pdb=" O PHE F 210 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE F 210 " --> pdb=" O TYR F 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 6 through 7 removed outlier: 4.055A pdb=" N SER I 7 " --> pdb=" O SER I 21 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU I 18 " --> pdb=" O MET I 82 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER I 77 " --> pdb=" O GLU I 72 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR I 68 " --> pdb=" O GLN I 81 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.625A pdb=" N ALA I 91 " --> pdb=" O VAL I 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AB9, first strand: chain 'H' and resid 35 through 37 removed outlier: 7.239A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.802A pdb=" N ARG H 65 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR H 72 " --> pdb=" O ARG H 65 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER H 67 " --> pdb=" O ASP H 70 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'H' and resid 117 through 119 removed outlier: 3.521A pdb=" N VAL H 134 " --> pdb=" O PHE H 119 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR H 174 " --> pdb=" O ASN H 139 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 155 through 156 removed outlier: 4.138A pdb=" N TRP H 149 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR H 193 " --> pdb=" O PHE H 210 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE H 210 " --> pdb=" O TYR H 193 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.618A pdb=" N PHE B 88 " --> pdb=" O PHE C 592 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 92 through 96 removed outlier: 3.655A pdb=" N THR B 92 " --> pdb=" O TYR B 307 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 144 through 145 removed outlier: 3.514A pdb=" N ASN B 271 " --> pdb=" O GLY B 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.615A pdb=" N ILE B 158 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 165 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 204 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AC9, first strand: chain 'B' and resid 224 through 225 removed outlier: 6.290A pdb=" N LEU B 235 " --> pdb=" O LYS B 262 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS B 262 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL B 237 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 339 through 342 removed outlier: 3.839A pdb=" N THR B 626 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 346 through 347 removed outlier: 3.512A pdb=" N GLY B 620 " --> pdb=" O PHE B 346 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 353 through 354 removed outlier: 7.706A pdb=" N VAL B 354 " --> pdb=" O ASN B 569 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 568 " --> pdb=" O GLY B 575 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 575 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 383 through 386 removed outlier: 3.525A pdb=" N LYS B 384 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 425 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 386 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL B 423 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS B 460 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 480 through 482 removed outlier: 3.579A pdb=" N ASN B 520 " --> pdb=" O TYR B 481 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 592 through 594 removed outlier: 7.154A pdb=" N GLY B 593 " --> pdb=" O ASP B 601 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 691 through 694 removed outlier: 3.959A pdb=" N ILE B 693 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE B 697 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 700 " --> pdb=" O VAL B 716 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 724 through 725 removed outlier: 6.373A pdb=" N ALA B 724 " --> pdb=" O MET A 811 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 741 through 751 Processing sheet with id=AE2, first strand: chain 'B' and resid 757 through 759 Processing sheet with id=AE3, first strand: chain 'B' and resid 810 through 811 Processing sheet with id=AE4, first strand: chain 'B' and resid 819 through 820 removed outlier: 3.570A pdb=" N PHE B 820 " --> pdb=" O PHE B 823 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1111 through 1113 removed outlier: 3.788A pdb=" N PHE B1112 " --> pdb=" O PHE B1144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 92 through 96 removed outlier: 3.698A pdb=" N VAL A 317 " --> pdb=" O MET A 304 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 130 through 132 removed outlier: 3.604A pdb=" N LEU A 223 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 130 through 132 removed outlier: 3.604A pdb=" N LEU A 223 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL A 237 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 158 through 159 removed outlier: 3.828A pdb=" N VAL A 164 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 339 through 347 removed outlier: 6.075A pdb=" N ILE A 340 " --> pdb=" O THR A 626 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR A 626 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLN A 342 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 624 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER A 344 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY A 620 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 353 through 356 Processing sheet with id=AF3, first strand: chain 'A' and resid 383 through 386 removed outlier: 3.833A pdb=" N LYS A 384 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 425 " --> pdb=" O LYS A 384 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 386 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 423 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS A 460 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 480 through 482 Processing sheet with id=AF5, first strand: chain 'A' and resid 600 through 603 removed outlier: 7.466A pdb=" N PHE A 592 " --> pdb=" O PHE C 88 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.583A pdb=" N SER A 700 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 718 " --> pdb=" O CYS A 698 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N CYS A 698 " --> pdb=" O TYR A 718 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA A 699 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 724 through 725 removed outlier: 6.071A pdb=" N ALA A 724 " --> pdb=" O MET C 811 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'A' and resid 735 through 751 removed outlier: 3.604A pdb=" N ARG A1096 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLN A1094 " --> pdb=" O THR A 739 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE A 741 " --> pdb=" O PRO A1092 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE A 743 " --> pdb=" O TYR A1090 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N TYR A1090 " --> pdb=" O ILE A 743 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE A 745 " --> pdb=" O VAL A1088 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A1088 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR A 747 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU A1086 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A 749 " --> pdb=" O VAL A1084 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A1084 " --> pdb=" O VAL A 749 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLY A1082 " --> pdb=" O PRO A 751 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 756 through 759 removed outlier: 4.341A pdb=" N LYS A 756 " --> pdb=" O LEU A 884 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AG2, first strand: chain 'A' and resid 863 through 864 Processing sheet with id=AG3, first strand: chain 'A' and resid 1104 through 1105 removed outlier: 3.658A pdb=" N CYS A1105 " --> pdb=" O ILE A1156 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'A' and resid 1111 through 1113 removed outlier: 3.717A pdb=" N PHE A1112 " --> pdb=" O PHE A1144 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 92 through 96 Processing sheet with id=AG6, first strand: chain 'C' and resid 204 through 207 removed outlier: 4.118A pdb=" N TYR C 204 " --> pdb=" O ILE C 166 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AG8, first strand: chain 'C' and resid 224 through 225 removed outlier: 7.156A pdb=" N VAL C 237 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 339 through 347 removed outlier: 3.666A pdb=" N THR C 626 " --> pdb=" O GLY C 339 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR C 343 " --> pdb=" O VAL C 622 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL C 622 " --> pdb=" O THR C 343 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASN C 345 " --> pdb=" O GLY C 620 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLY C 620 " --> pdb=" O ASN C 345 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 353 through 355 Processing sheet with id=AH2, first strand: chain 'C' and resid 383 through 386 removed outlier: 3.760A pdb=" N LYS C 384 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 425 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 423 " --> pdb=" O ILE C 386 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN C 422 " --> pdb=" O GLU C 543 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS C 460 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 480 through 482 removed outlier: 3.508A pdb=" N ASN C 520 " --> pdb=" O TYR C 481 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 691 through 694 removed outlier: 3.888A pdb=" N ILE C 693 " --> pdb=" O ILE C 697 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE C 697 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER C 700 " --> pdb=" O VAL C 716 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AH6, first strand: chain 'C' and resid 741 through 751 Processing sheet with id=AH7, first strand: chain 'C' and resid 757 through 759 Processing sheet with id=AH8, first strand: chain 'C' and resid 819 through 820 Processing sheet with id=AH9, first strand: chain 'C' and resid 863 through 864 Processing sheet with id=AI1, first strand: chain 'C' and resid 1104 through 1105 removed outlier: 4.011A pdb=" N CYS C1105 " --> pdb=" O ILE C1156 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'C' and resid 1111 through 1113 removed outlier: 3.791A pdb=" N PHE C1112 " --> pdb=" O PHE C1144 " (cutoff:3.500A) 890 hydrogen bonds defined for protein. 2436 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.11 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10377 1.34 - 1.46: 6091 1.46 - 1.58: 18467 1.58 - 1.70: 0 1.70 - 1.82: 222 Bond restraints: 35157 Sorted by residual: bond pdb=" N ILE C 360 " pdb=" CA ILE C 360 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.08e-02 8.57e+03 1.28e+01 bond pdb=" N ILE B 360 " pdb=" CA ILE B 360 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N VAL F 116 " pdb=" CA VAL F 116 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.75e+00 bond pdb=" N VAL E 118 " pdb=" CA VAL E 118 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.08e-02 8.57e+03 9.00e+00 bond pdb=" N ILE A 360 " pdb=" CA ILE A 360 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.74e+00 ... (remaining 35152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 47061 1.89 - 3.78: 711 3.78 - 5.67: 45 5.67 - 7.56: 14 7.56 - 9.45: 1 Bond angle restraints: 47832 Sorted by residual: angle pdb=" C THR B 558 " pdb=" CA THR B 558 " pdb=" CB THR B 558 " ideal model delta sigma weight residual 114.10 104.65 9.45 2.11e+00 2.25e-01 2.01e+01 angle pdb=" C SER G 121 " pdb=" CA SER G 121 " pdb=" CB SER G 121 " ideal model delta sigma weight residual 116.54 111.41 5.13 1.15e+00 7.56e-01 1.99e+01 angle pdb=" C SER I 121 " pdb=" CA SER I 121 " pdb=" CB SER I 121 " ideal model delta sigma weight residual 116.54 111.65 4.89 1.15e+00 7.56e-01 1.81e+01 angle pdb=" CA GLY B 553 " pdb=" C GLY B 553 " pdb=" O GLY B 553 " ideal model delta sigma weight residual 122.46 118.41 4.05 9.70e-01 1.06e+00 1.75e+01 angle pdb=" CA THR C 361 " pdb=" C THR C 361 " pdb=" O THR C 361 " ideal model delta sigma weight residual 121.84 117.34 4.50 1.16e+00 7.43e-01 1.51e+01 ... (remaining 47827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 20051 17.73 - 35.46: 748 35.46 - 53.19: 127 53.19 - 70.92: 31 70.92 - 88.65: 10 Dihedral angle restraints: 20967 sinusoidal: 8082 harmonic: 12885 Sorted by residual: dihedral pdb=" CA LYS B 555 " pdb=" C LYS B 555 " pdb=" N LEU B 556 " pdb=" CA LEU B 556 " ideal model delta harmonic sigma weight residual -180.00 -155.62 -24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA SER E 121 " pdb=" C SER E 121 " pdb=" N SER E 122 " pdb=" CA SER E 122 " ideal model delta harmonic sigma weight residual -180.00 -159.79 -20.21 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ALA A 512 " pdb=" C ALA A 512 " pdb=" N LEU A 513 " pdb=" CA LEU A 513 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 20964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4440 0.053 - 0.105: 785 0.105 - 0.158: 162 0.158 - 0.211: 18 0.211 - 0.264: 1 Chirality restraints: 5406 Sorted by residual: chirality pdb=" CA ILE B 561 " pdb=" N ILE B 561 " pdb=" C ILE B 561 " pdb=" CB ILE B 561 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA VAL F 111 " pdb=" N VAL F 111 " pdb=" C VAL F 111 " pdb=" CB VAL F 111 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA VAL D 111 " pdb=" N VAL D 111 " pdb=" C VAL D 111 " pdb=" CB VAL D 111 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 5403 not shown) Planarity restraints: 6174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 356 " 0.252 9.50e-02 1.11e+02 1.13e-01 7.80e+00 pdb=" NE ARG B 356 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 356 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 356 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 356 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 604 " 0.229 9.50e-02 1.11e+02 1.03e-01 6.45e+00 pdb=" NE ARG C 604 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 604 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 604 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 604 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B1008 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO B1009 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B1009 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B1009 " 0.028 5.00e-02 4.00e+02 ... (remaining 6171 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3246 2.75 - 3.29: 33521 3.29 - 3.83: 55621 3.83 - 4.36: 62354 4.36 - 4.90: 109245 Nonbonded interactions: 263987 Sorted by model distance: nonbonded pdb=" O PHE A 144 " pdb=" OG SER A 154 " model vdw 2.215 3.040 nonbonded pdb=" OD2 ASP B 318 " pdb=" OG SER B 320 " model vdw 2.261 3.040 nonbonded pdb=" OG SER C 700 " pdb=" OH TYR C 718 " model vdw 2.270 3.040 nonbonded pdb=" O SER B 960 " pdb=" OG1 THR B 964 " model vdw 2.274 3.040 nonbonded pdb=" O SER C 960 " pdb=" OG1 THR C 964 " model vdw 2.276 3.040 ... (remaining 263982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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 individual isotropic 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.820 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 : 0.003 0.042 35211 Z= 0.192 Angle : 0.511 9.449 47940 Z= 0.305 Chirality : 0.043 0.264 5406 Planarity : 0.004 0.113 6174 Dihedral : 9.376 88.648 12543 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.04 % Favored : 92.69 % Rotamer: Outliers : 5.28 % Allowed : 6.75 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.11), residues: 4392 helix: 0.97 (0.19), residues: 661 sheet: -2.64 (0.14), residues: 1054 loop : -3.78 (0.09), residues: 2677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 109 TYR 0.004 0.000 TYR D 141 PHE 0.008 0.001 PHE B 357 TRP 0.006 0.000 TRP A 464 HIS 0.003 0.000 HIS C1071 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.19 (35157) covalent geometry : angle 0.51078 / 0.31 (47832) SS BOND : bond 0.00131 / 0.09 ( 54) SS BOND : angle 0.53052 / 0.32 ( 108) hydrogen bonds : bond 0.21314 / 14.20 ( 879) hydrogen bonds : angle 8.20286 / 5.46 ( 2436) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 377 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 85 LEU cc_start: -0.0546 (OUTLIER) cc_final: -0.1193 (tp) REVERT: E 90 THR cc_start: 0.7582 (OUTLIER) cc_final: 0.7282 (m) REVERT: D 135 CYS cc_start: 0.7726 (t) cc_final: 0.7420 (p) REVERT: G 63 VAL cc_start: 0.5223 (OUTLIER) cc_final: 0.4246 (p) REVERT: F 35 TRP cc_start: 0.6931 (OUTLIER) cc_final: 0.6438 (t-100) REVERT: F 115 SER cc_start: 0.5719 (OUTLIER) cc_final: 0.5460 (p) REVERT: I 28 THR cc_start: 0.8935 (m) cc_final: 0.8639 (t) REVERT: I 90 THR cc_start: 0.7289 (OUTLIER) cc_final: 0.6686 (m) REVERT: I 117 ARG cc_start: 0.6468 (OUTLIER) cc_final: 0.6188 (mtt-85) REVERT: H 35 TRP cc_start: 0.3810 (OUTLIER) cc_final: 0.1927 (m100) REVERT: B 192 MET cc_start: 0.5783 (mmt) cc_final: 0.4896 (mmt) REVERT: B 293 TYR cc_start: 0.7027 (m-10) cc_final: 0.6667 (m-10) REVERT: B 298 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6421 (pp) REVERT: B 508 CYS cc_start: 0.1484 (OUTLIER) cc_final: 0.1159 (t) REVERT: B 782 PHE cc_start: 0.7343 (m-80) cc_final: 0.6188 (m-80) REVERT: B 1109 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8834 (pttm) REVERT: A 192 MET cc_start: 0.4609 (mmt) cc_final: 0.4313 (mmt) REVERT: A 400 THR cc_start: 0.5477 (OUTLIER) cc_final: 0.5129 (m) REVERT: A 952 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8848 (tppt) REVERT: C 192 MET cc_start: 0.4950 (mmt) cc_final: 0.4647 (mmt) REVERT: C 235 LEU cc_start: 0.9182 (tp) cc_final: 0.8940 (tt) REVERT: C 400 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7771 (m) REVERT: C 508 CYS cc_start: 0.3806 (OUTLIER) cc_final: 0.3403 (t) REVERT: C 641 ASP cc_start: 0.8161 (m-30) cc_final: 0.7862 (m-30) REVERT: C 824 ASN cc_start: 0.6658 (OUTLIER) cc_final: 0.6430 (t0) outliers start: 202 outliers final: 41 residues processed: 561 average time/residue: 0.2198 time to fit residues: 195.9429 Evaluate side-chains 244 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 187 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 117 ARG Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 142 TRP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 712 GLN Chi-restraints excluded: chain B residue 761 CYS Chi-restraints excluded: chain B residue 1109 LYS Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 142 TRP Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 508 CYS Chi-restraints excluded: chain C residue 607 LYS Chi-restraints excluded: chain C residue 676 CYS Chi-restraints excluded: chain C residue 761 CYS Chi-restraints excluded: chain C residue 824 ASN Chi-restraints excluded: chain C residue 1109 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.3980 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 20 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.0116 > 50:) chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 7.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 13 GLN E 171 HIS D 34 ASN D 89 GLN D 101 GLN G 13 GLN G 171 HIS G 178 GLN F 34 ASN F 89 GLN F 101 GLN I 13 GLN ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 HIS H 34 ASN H 89 GLN H 101 GLN H 148 GLN B 119 ASN B 149 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN B 362 ASN B 437 GLN B 520 ASN B 587 GLN B 591 GLN B 673 GLN B 876 GLN B 983 ASN ** B1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1087 HIS B1165 GLN A 170 ASN A 242 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 ASN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN A 673 GLN A 682 HIS ** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 GLN A1087 HIS A1165 GLN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN C 437 GLN C 520 ASN C 546 ASN C 587 GLN ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C 876 GLN C 937 ASN ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1087 HIS C1165 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.106885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.065017 restraints weight = 147309.900| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 5.81 r_work: 0.3125 rms_B_bonded: 5.23 restraints_weight: 2.0000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 35211 Z= 0.210 Angle : 0.615 10.378 47940 Z= 0.315 Chirality : 0.044 0.213 5406 Planarity : 0.004 0.067 6174 Dihedral : 5.574 78.574 4892 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.56 % Favored : 91.37 % Rotamer: Outliers : 3.50 % Allowed : 9.78 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.12), residues: 4392 helix: 1.76 (0.20), residues: 682 sheet: -2.24 (0.14), residues: 1146 loop : -3.43 (0.10), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1130 TYR 0.023 0.001 TYR I 108 PHE 0.040 0.002 PHE H 71 TRP 0.031 0.001 TRP H 35 HIS 0.005 0.001 HIS C1071 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (35157) covalent geometry : angle 0.61380 / 0.31 (47832) SS BOND : bond 0.00602 / 0.30 ( 54) SS BOND : angle 0.90898 / 0.53 ( 108) hydrogen bonds : bond 0.03957 / 2.59 ( 879) hydrogen bonds : angle 5.77586 / 3.84 ( 2436) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 176 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 THR cc_start: 0.7703 (OUTLIER) cc_final: 0.7457 (m) REVERT: F 35 TRP cc_start: 0.7401 (OUTLIER) cc_final: 0.6496 (t-100) REVERT: B 205 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.9108 (mp) REVERT: B 438 ILE cc_start: 0.2628 (OUTLIER) cc_final: 0.2359 (mm) REVERT: B 866 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7592 (p0) REVERT: B 1109 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8777 (pttm) REVERT: B 1149 CYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7965 (m) REVERT: A 192 MET cc_start: 0.4552 (mmt) cc_final: 0.4051 (mmt) REVERT: A 400 THR cc_start: 0.5491 (OUTLIER) cc_final: 0.5193 (m) REVERT: A 598 ASP cc_start: 0.8903 (t0) cc_final: 0.8692 (t0) REVERT: A 642 VAL cc_start: 0.9487 (OUTLIER) cc_final: 0.9266 (m) REVERT: A 673 GLN cc_start: 0.8296 (tm-30) cc_final: 0.8000 (tm-30) REVERT: A 712 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8016 (pp30) REVERT: A 952 LYS cc_start: 0.9514 (OUTLIER) cc_final: 0.9224 (tppt) REVERT: A 1064 ASP cc_start: 0.8845 (t0) cc_final: 0.8524 (t0) REVERT: C 235 LEU cc_start: 0.9565 (tp) cc_final: 0.9308 (tt) REVERT: C 304 MET cc_start: 0.8964 (ttt) cc_final: 0.8686 (ttt) REVERT: C 361 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8207 (p) outliers start: 134 outliers final: 58 residues processed: 298 average time/residue: 0.1894 time to fit residues: 93.7057 Evaluate side-chains 218 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 148 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 142 TRP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 761 CYS Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1109 LYS Chi-restraints excluded: chain B residue 1149 CYS Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1149 CYS Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 142 TRP Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 761 CYS Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1109 LYS Chi-restraints excluded: chain C residue 1149 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 221 optimal weight: 0.8980 chunk 382 optimal weight: 0.0970 chunk 63 optimal weight: 50.0000 chunk 350 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 427 optimal weight: 1.9990 chunk 154 optimal weight: 30.0000 chunk 236 optimal weight: 4.9990 chunk 409 optimal weight: 7.9990 chunk 379 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 148 GLN B 153 GLN B 362 ASN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 ASN B 937 ASN A 196 ASN A 437 GLN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN A 936 GLN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 785 GLN ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.108132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.068511 restraints weight = 152607.596| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 5.31 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35211 Z= 0.109 Angle : 0.546 10.343 47940 Z= 0.272 Chirality : 0.042 0.203 5406 Planarity : 0.004 0.064 6174 Dihedral : 4.934 73.018 4849 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.95 % Favored : 91.99 % Rotamer: Outliers : 3.03 % Allowed : 9.78 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.12), residues: 4392 helix: 2.18 (0.20), residues: 683 sheet: -1.93 (0.15), residues: 1113 loop : -3.28 (0.10), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1130 TYR 0.021 0.001 TYR A 927 PHE 0.032 0.001 PHE C 124 TRP 0.014 0.001 TRP A 909 HIS 0.003 0.000 HIS C1087 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (35157) covalent geometry : angle 0.54607 / 0.27 (47832) SS BOND : bond 0.00193 / 0.12 ( 54) SS BOND : angle 0.63018 / 0.40 ( 108) hydrogen bonds : bond 0.03352 / 2.19 ( 879) hydrogen bonds : angle 5.27140 / 3.49 ( 2436) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 160 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 ASP cc_start: 0.8549 (m-30) cc_final: 0.8228 (m-30) REVERT: G 82 MET cc_start: 0.0267 (mmm) cc_final: -0.0152 (mmp) REVERT: F 24 ARG cc_start: 0.9237 (mtm110) cc_final: 0.8737 (ptt-90) REVERT: F 35 TRP cc_start: 0.7336 (OUTLIER) cc_final: 0.6545 (t-100) REVERT: B 205 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9014 (mp) REVERT: B 231 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8989 (pttp) REVERT: B 866 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7691 (p0) REVERT: B 1074 SER cc_start: 0.8957 (t) cc_final: 0.8664 (m) REVERT: B 1109 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8823 (pttm) REVERT: A 192 MET cc_start: 0.4403 (mmt) cc_final: 0.4038 (mmt) REVERT: A 400 THR cc_start: 0.5476 (OUTLIER) cc_final: 0.5147 (m) REVERT: A 598 ASP cc_start: 0.8698 (t0) cc_final: 0.8389 (t0) REVERT: A 642 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.9093 (m) REVERT: A 673 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7969 (tm-30) REVERT: A 712 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8091 (pp30) REVERT: A 857 MET cc_start: 0.8898 (tmm) cc_final: 0.8570 (pmm) REVERT: A 923 MET cc_start: 0.9130 (mtm) cc_final: 0.8818 (mtm) REVERT: A 952 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.9047 (tppt) REVERT: A 1064 ASP cc_start: 0.8312 (t0) cc_final: 0.8073 (t0) REVERT: A 1149 CYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7580 (m) REVERT: C 235 LEU cc_start: 0.9553 (tp) cc_final: 0.9332 (tt) REVERT: C 297 TYR cc_start: 0.8184 (m-80) cc_final: 0.7933 (m-10) REVERT: C 304 MET cc_start: 0.8480 (ttt) cc_final: 0.8101 (ttt) REVERT: C 1074 SER cc_start: 0.9122 (t) cc_final: 0.8675 (p) outliers start: 116 outliers final: 71 residues processed: 267 average time/residue: 0.2028 time to fit residues: 89.3800 Evaluate side-chains 232 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 151 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 142 TRP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 761 CYS Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1109 LYS Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain A residue 142 TRP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1149 CYS Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 142 TRP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 761 CYS Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 1109 LYS Chi-restraints excluded: chain C residue 1149 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 22 optimal weight: 1.9990 chunk 155 optimal weight: 40.0000 chunk 184 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 370 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 112 optimal weight: 50.0000 chunk 127 optimal weight: 0.3980 chunk 396 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 160 optimal weight: 8.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 125 GLN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN B 682 HIS B 712 GLN B 785 GLN B 918 GLN ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 GLN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 640 GLN A 673 GLN ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 GLN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 GLN C 673 GLN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 GLN C 988 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.103798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.059634 restraints weight = 137594.783| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 5.45 r_work: 0.2945 rms_B_bonded: 5.13 restraints_weight: 2.0000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 35211 Z= 0.252 Angle : 0.652 10.876 47940 Z= 0.333 Chirality : 0.044 0.256 5406 Planarity : 0.004 0.059 6174 Dihedral : 5.365 61.286 4848 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.02 % Favored : 89.89 % Rotamer: Outliers : 3.58 % Allowed : 9.88 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.12), residues: 4392 helix: 1.59 (0.20), residues: 721 sheet: -1.81 (0.15), residues: 1085 loop : -3.10 (0.10), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1062 TYR 0.018 0.001 TYR C 204 PHE 0.027 0.002 PHE A1098 TRP 0.018 0.001 TRP A 909 HIS 0.010 0.001 HIS A1071 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.25 (35157) covalent geometry : angle 0.65124 / 0.33 (47832) SS BOND : bond 0.00408 / 0.25 ( 54) SS BOND : angle 0.87386 / 0.56 ( 108) hydrogen bonds : bond 0.04129 / 2.71 ( 879) hydrogen bonds : angle 5.18637 / 3.46 ( 2436) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 162 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 ASP cc_start: 0.8600 (m-30) cc_final: 0.8282 (m-30) REVERT: G 82 MET cc_start: 0.0159 (mmm) cc_final: -0.0306 (mmt) REVERT: F 24 ARG cc_start: 0.9308 (mtm110) cc_final: 0.8859 (ptt-90) REVERT: F 35 TRP cc_start: 0.7387 (OUTLIER) cc_final: 0.6604 (t-100) REVERT: B 142 TRP cc_start: 0.8495 (OUTLIER) cc_final: 0.8270 (m-10) REVERT: B 148 MET cc_start: 0.7810 (mmt) cc_final: 0.7485 (mmm) REVERT: B 231 LYS cc_start: 0.9460 (OUTLIER) cc_final: 0.9220 (pttp) REVERT: B 267 ILE cc_start: 0.5930 (OUTLIER) cc_final: 0.5728 (pt) REVERT: B 614 ILE cc_start: 0.7741 (pt) cc_final: 0.7538 (pt) REVERT: B 866 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7765 (p0) REVERT: A 192 MET cc_start: 0.4524 (mmt) cc_final: 0.4034 (mmt) REVERT: A 400 THR cc_start: 0.5687 (OUTLIER) cc_final: 0.5431 (m) REVERT: A 598 ASP cc_start: 0.9213 (t0) cc_final: 0.8923 (t0) REVERT: A 642 VAL cc_start: 0.9366 (OUTLIER) cc_final: 0.9130 (m) REVERT: A 671 GLN cc_start: 0.7641 (mp10) cc_final: 0.7368 (mp10) REVERT: A 712 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7877 (pp30) REVERT: A 754 MET cc_start: 0.9349 (ptm) cc_final: 0.9133 (ptp) REVERT: A 952 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.9221 (tppt) REVERT: A 1064 ASP cc_start: 0.9166 (t0) cc_final: 0.8788 (t0) REVERT: C 598 ASP cc_start: 0.9361 (t70) cc_final: 0.8690 (t0) REVERT: C 638 LEU cc_start: 0.9530 (tp) cc_final: 0.9193 (tt) REVERT: C 655 GLN cc_start: 0.9482 (OUTLIER) cc_final: 0.8980 (mm110) REVERT: C 892 MET cc_start: 0.9681 (mtm) cc_final: 0.9400 (mtm) REVERT: C 982 LEU cc_start: 0.9756 (OUTLIER) cc_final: 0.9548 (mm) REVERT: C 1074 SER cc_start: 0.9326 (t) cc_final: 0.9009 (p) REVERT: C 1127 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8104 (mt) outliers start: 137 outliers final: 79 residues processed: 284 average time/residue: 0.2127 time to fit residues: 100.3000 Evaluate side-chains 235 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 144 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 142 TRP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 757 THR Chi-restraints excluded: chain B residue 761 CYS Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1109 LYS Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1149 CYS Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain A residue 142 TRP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1149 CYS Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 142 TRP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 655 GLN Chi-restraints excluded: chain C residue 761 CYS Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1109 LYS Chi-restraints excluded: chain C residue 1120 PHE Chi-restraints excluded: chain C residue 1127 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 218 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 400 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 304 optimal weight: 0.1980 chunk 268 optimal weight: 30.0000 chunk 166 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 300 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 37 HIS H 38 GLN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 GLN B 918 GLN ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN A 702 HIS ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 ASN C 119 ASN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.105036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.062418 restraints weight = 145972.260| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 5.80 r_work: 0.2975 rms_B_bonded: 5.77 restraints_weight: 2.0000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35211 Z= 0.131 Angle : 0.570 12.223 47940 Z= 0.286 Chirality : 0.042 0.179 5406 Planarity : 0.004 0.058 6174 Dihedral : 5.143 52.446 4846 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.58 % Favored : 91.35 % Rotamer: Outliers : 2.95 % Allowed : 11.14 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.12), residues: 4392 helix: 1.84 (0.20), residues: 727 sheet: -1.63 (0.15), residues: 1087 loop : -2.98 (0.11), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1062 TYR 0.013 0.001 TYR C 293 PHE 0.026 0.001 PHE A 124 TRP 0.014 0.001 TRP A 909 HIS 0.004 0.001 HIS A1071 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (35157) covalent geometry : angle 0.56873 / 0.29 (47832) SS BOND : bond 0.00339 / 0.24 ( 54) SS BOND : angle 0.87550 / 0.56 ( 108) hydrogen bonds : bond 0.03421 / 2.23 ( 879) hydrogen bonds : angle 4.87185 / 3.25 ( 2436) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 155 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 MET cc_start: 0.0469 (mmm) cc_final: 0.0037 (mtt) REVERT: G 73 ASP cc_start: 0.8486 (m-30) cc_final: 0.8162 (m-30) REVERT: F 24 ARG cc_start: 0.9335 (mtm110) cc_final: 0.8922 (ptt-90) REVERT: F 35 TRP cc_start: 0.7347 (OUTLIER) cc_final: 0.6588 (t-100) REVERT: B 99 LEU cc_start: 0.9231 (tp) cc_final: 0.9021 (tt) REVERT: B 148 MET cc_start: 0.7292 (mmt) cc_final: 0.6954 (mmm) REVERT: B 293 TYR cc_start: 0.7942 (m-10) cc_final: 0.7489 (m-10) REVERT: B 866 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7776 (p0) REVERT: B 1149 CYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8204 (m) REVERT: A 148 MET cc_start: 0.8308 (mmp) cc_final: 0.6936 (ttt) REVERT: A 192 MET cc_start: 0.4477 (mmt) cc_final: 0.4093 (mmt) REVERT: A 400 THR cc_start: 0.5797 (OUTLIER) cc_final: 0.5580 (m) REVERT: A 598 ASP cc_start: 0.9199 (t0) cc_final: 0.8870 (t0) REVERT: A 642 VAL cc_start: 0.9407 (OUTLIER) cc_final: 0.9190 (m) REVERT: A 712 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7901 (pp30) REVERT: A 857 MET cc_start: 0.8911 (tmm) cc_final: 0.8552 (pmm) REVERT: A 892 MET cc_start: 0.9669 (mtt) cc_final: 0.9467 (mtt) REVERT: A 952 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.9223 (tppt) REVERT: A 1064 ASP cc_start: 0.9111 (t0) cc_final: 0.8630 (t0) REVERT: C 235 LEU cc_start: 0.9641 (tp) cc_final: 0.9357 (tt) REVERT: C 598 ASP cc_start: 0.9374 (t70) cc_final: 0.8712 (t0) outliers start: 113 outliers final: 73 residues processed: 260 average time/residue: 0.2047 time to fit residues: 88.7819 Evaluate side-chains 224 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 144 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 712 GLN Chi-restraints excluded: chain B residue 761 CYS Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1109 LYS Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1149 CYS Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1149 CYS Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 761 CYS Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 1109 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 399 optimal weight: 0.7980 chunk 65 optimal weight: 30.0000 chunk 184 optimal weight: 7.9990 chunk 16 optimal weight: 0.0270 chunk 275 optimal weight: 9.9990 chunk 293 optimal weight: 3.9990 chunk 403 optimal weight: 3.9990 chunk 18 optimal weight: 50.0000 chunk 17 optimal weight: 30.0000 chunk 158 optimal weight: 8.9990 chunk 255 optimal weight: 5.9990 overall best weight: 2.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 38 GLN G 35 HIS ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 945 GLN A 137 ASN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 945 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.103403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.059849 restraints weight = 145782.201| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 5.76 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 35211 Z= 0.216 Angle : 0.615 13.678 47940 Z= 0.311 Chirality : 0.043 0.177 5406 Planarity : 0.004 0.058 6174 Dihedral : 5.171 51.522 4840 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.81 % Favored : 90.10 % Rotamer: Outliers : 3.35 % Allowed : 11.32 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.12), residues: 4392 helix: 1.90 (0.20), residues: 722 sheet: -1.48 (0.16), residues: 1035 loop : -2.84 (0.11), residues: 2635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 66 TYR 0.017 0.001 TYR C 293 PHE 0.037 0.001 PHE B 124 TRP 0.032 0.001 TRP B 142 HIS 0.006 0.001 HIS C1071 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 (35157) covalent geometry : angle 0.61465 / 0.31 (47832) SS BOND : bond 0.00360 / 0.22 ( 54) SS BOND : angle 0.78797 / 0.50 ( 108) hydrogen bonds : bond 0.03559 / 2.32 ( 879) hydrogen bonds : angle 4.91250 / 3.27 ( 2436) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 145 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 MET cc_start: -0.0233 (mmm) cc_final: -0.0435 (mtt) REVERT: G 73 ASP cc_start: 0.8697 (m-30) cc_final: 0.8431 (m-30) REVERT: G 82 MET cc_start: 0.0559 (mmt) cc_final: 0.0120 (mmp) REVERT: F 24 ARG cc_start: 0.9332 (mtm110) cc_final: 0.8917 (ptt-90) REVERT: F 35 TRP cc_start: 0.7304 (OUTLIER) cc_final: 0.6428 (t-100) REVERT: F 47 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8376 (tm) REVERT: I 92 MET cc_start: 0.4064 (ppp) cc_final: 0.3837 (ppp) REVERT: B 148 MET cc_start: 0.8165 (mmt) cc_final: 0.7844 (mmm) REVERT: B 763 MET cc_start: 0.9457 (tpp) cc_final: 0.8852 (tpp) REVERT: B 866 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7732 (p0) REVERT: B 1149 CYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7368 (m) REVERT: A 192 MET cc_start: 0.4166 (mmt) cc_final: 0.3871 (mmt) REVERT: A 400 THR cc_start: 0.5573 (OUTLIER) cc_final: 0.5311 (m) REVERT: A 598 ASP cc_start: 0.9042 (t0) cc_final: 0.8701 (t0) REVERT: A 642 VAL cc_start: 0.9314 (OUTLIER) cc_final: 0.9101 (m) REVERT: A 712 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8058 (pp30) REVERT: A 782 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8635 (t80) REVERT: A 952 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9065 (tppt) REVERT: A 1118 PHE cc_start: 0.7058 (m-80) cc_final: 0.6793 (m-80) REVERT: A 1149 CYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7749 (m) REVERT: C 598 ASP cc_start: 0.9192 (t70) cc_final: 0.8458 (t0) REVERT: C 655 GLN cc_start: 0.9369 (OUTLIER) cc_final: 0.9065 (mm110) REVERT: C 673 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8751 (tp-100) REVERT: C 892 MET cc_start: 0.9553 (mtm) cc_final: 0.9248 (mtm) REVERT: C 1118 PHE cc_start: 0.7927 (m-80) cc_final: 0.7446 (m-80) outliers start: 128 outliers final: 81 residues processed: 260 average time/residue: 0.1948 time to fit residues: 84.7774 Evaluate side-chains 226 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 134 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 757 THR Chi-restraints excluded: chain B residue 761 CYS Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1109 LYS Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1149 CYS Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain A residue 142 TRP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1149 CYS Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 655 GLN Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 761 CYS Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 1109 LYS Chi-restraints excluded: chain C residue 1127 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 284 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 300 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 240 optimal weight: 20.0000 chunk 263 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 109 optimal weight: 30.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN B 153 GLN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 945 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.103379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.060587 restraints weight = 146764.835| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 5.89 r_work: 0.2913 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 35211 Z= 0.188 Angle : 0.603 14.443 47940 Z= 0.303 Chirality : 0.043 0.174 5406 Planarity : 0.004 0.058 6174 Dihedral : 5.134 50.399 4837 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.27 % Favored : 90.66 % Rotamer: Outliers : 3.01 % Allowed : 11.84 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.12), residues: 4392 helix: 1.90 (0.20), residues: 724 sheet: -1.42 (0.16), residues: 1085 loop : -2.76 (0.11), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 66 TYR 0.017 0.001 TYR C 293 PHE 0.029 0.001 PHE A 124 TRP 0.015 0.001 TRP A 909 HIS 0.005 0.001 HIS C1071 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (35157) covalent geometry : angle 0.60228 / 0.30 (47832) SS BOND : bond 0.00288 / 0.17 ( 54) SS BOND : angle 0.73173 / 0.46 ( 108) hydrogen bonds : bond 0.03452 / 2.26 ( 879) hydrogen bonds : angle 4.80467 / 3.20 ( 2436) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 142 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 MET cc_start: 0.0405 (mmm) cc_final: 0.0161 (mtt) REVERT: G 73 ASP cc_start: 0.8714 (m-30) cc_final: 0.8430 (m-30) REVERT: G 82 MET cc_start: 0.0556 (mmt) cc_final: -0.0036 (mmp) REVERT: F 35 TRP cc_start: 0.7294 (OUTLIER) cc_final: 0.6364 (t-100) REVERT: F 47 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8421 (tm) REVERT: B 148 MET cc_start: 0.7939 (mmt) cc_final: 0.7451 (mmm) REVERT: B 763 MET cc_start: 0.9672 (tpp) cc_final: 0.9097 (tpp) REVERT: B 866 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7762 (p0) REVERT: B 1109 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8902 (pttm) REVERT: B 1149 CYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8248 (m) REVERT: A 192 MET cc_start: 0.4430 (mmt) cc_final: 0.4050 (mmt) REVERT: A 400 THR cc_start: 0.5348 (OUTLIER) cc_final: 0.5107 (m) REVERT: A 598 ASP cc_start: 0.9301 (t0) cc_final: 0.8987 (t0) REVERT: A 712 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7927 (pp30) REVERT: A 892 MET cc_start: 0.9738 (mtt) cc_final: 0.9525 (mtt) REVERT: A 952 LYS cc_start: 0.9506 (OUTLIER) cc_final: 0.9195 (tppt) REVERT: A 1064 ASP cc_start: 0.9151 (t0) cc_final: 0.8930 (t0) REVERT: A 1118 PHE cc_start: 0.7555 (m-80) cc_final: 0.7257 (m-80) REVERT: A 1149 CYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8399 (m) REVERT: C 148 MET cc_start: 0.8300 (mmt) cc_final: 0.8013 (mmt) REVERT: C 235 LEU cc_start: 0.9652 (tp) cc_final: 0.9274 (tt) REVERT: C 263 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8205 (pt) REVERT: C 638 LEU cc_start: 0.9463 (tt) cc_final: 0.9263 (tt) REVERT: C 655 GLN cc_start: 0.9416 (OUTLIER) cc_final: 0.9197 (mm110) REVERT: C 1118 PHE cc_start: 0.8394 (m-80) cc_final: 0.8001 (m-80) outliers start: 115 outliers final: 81 residues processed: 246 average time/residue: 0.1925 time to fit residues: 78.0091 Evaluate side-chains 230 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 138 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 757 THR Chi-restraints excluded: chain B residue 761 CYS Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1109 LYS Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain B residue 1130 ARG Chi-restraints excluded: chain B residue 1149 CYS Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1149 CYS Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 655 GLN Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 761 CYS Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 1109 LYS Chi-restraints excluded: chain C residue 1127 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 186 optimal weight: 0.8980 chunk 432 optimal weight: 0.0970 chunk 411 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 chunk 385 optimal weight: 0.3980 chunk 308 optimal weight: 0.9980 chunk 204 optimal weight: 0.2980 chunk 69 optimal weight: 4.9990 chunk 115 optimal weight: 0.4980 chunk 344 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN B 153 GLN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B 945 GLN A 571 ASN A 673 GLN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 945 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.105471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.064293 restraints weight = 151705.115| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 5.12 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 35211 Z= 0.100 Angle : 0.583 14.452 47940 Z= 0.286 Chirality : 0.043 0.177 5406 Planarity : 0.004 0.059 6174 Dihedral : 4.948 48.378 4837 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.93 % Favored : 91.01 % Rotamer: Outliers : 2.51 % Allowed : 12.44 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.13), residues: 4392 helix: 2.12 (0.20), residues: 720 sheet: -1.13 (0.16), residues: 1105 loop : -2.67 (0.11), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 66 TYR 0.021 0.001 TYR C 927 PHE 0.032 0.001 PHE A 124 TRP 0.018 0.001 TRP B 909 HIS 0.004 0.000 HIS B1087 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (35157) covalent geometry : angle 0.58235 / 0.29 (47832) SS BOND : bond 0.00199 / 0.12 ( 54) SS BOND : angle 0.69117 / 0.45 ( 108) hydrogen bonds : bond 0.02969 / 1.93 ( 879) hydrogen bonds : angle 4.49743 / 3.00 ( 2436) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 157 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 MET cc_start: -0.0523 (mmm) cc_final: -0.0744 (mtt) REVERT: G 73 ASP cc_start: 0.8533 (m-30) cc_final: 0.8233 (m-30) REVERT: G 82 MET cc_start: 0.0175 (mmt) cc_final: -0.0227 (mmt) REVERT: F 35 TRP cc_start: 0.7294 (OUTLIER) cc_final: 0.6421 (t-100) REVERT: F 47 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8389 (tm) REVERT: F 70 ASP cc_start: 0.9537 (t0) cc_final: 0.9270 (p0) REVERT: I 92 MET cc_start: 0.4574 (ppp) cc_final: 0.4327 (ppp) REVERT: B 148 MET cc_start: 0.7717 (mmt) cc_final: 0.7392 (mmm) REVERT: B 317 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8720 (p) REVERT: B 655 GLN cc_start: 0.9437 (OUTLIER) cc_final: 0.9080 (mm110) REVERT: B 720 MET cc_start: 0.8459 (ttp) cc_final: 0.8221 (ttm) REVERT: B 866 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7925 (p0) REVERT: B 892 MET cc_start: 0.9347 (mtp) cc_final: 0.9026 (mtm) REVERT: B 927 TYR cc_start: 0.8733 (t80) cc_final: 0.8427 (t80) REVERT: B 1109 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8855 (pttm) REVERT: A 192 MET cc_start: 0.4415 (mmt) cc_final: 0.4117 (mmt) REVERT: A 378 VAL cc_start: 0.1985 (OUTLIER) cc_final: 0.1771 (m) REVERT: A 400 THR cc_start: 0.5398 (OUTLIER) cc_final: 0.5128 (m) REVERT: A 598 ASP cc_start: 0.8982 (t0) cc_final: 0.8586 (t0) REVERT: A 892 MET cc_start: 0.9589 (mtt) cc_final: 0.9261 (mtt) REVERT: A 952 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9141 (tppt) REVERT: A 1064 ASP cc_start: 0.8650 (t0) cc_final: 0.8377 (t0) REVERT: A 1074 SER cc_start: 0.9443 (t) cc_final: 0.9115 (p) REVERT: A 1149 CYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7893 (m) REVERT: C 235 LEU cc_start: 0.9628 (tp) cc_final: 0.9330 (tt) REVERT: C 297 TYR cc_start: 0.7984 (m-80) cc_final: 0.7575 (m-80) REVERT: C 598 ASP cc_start: 0.9211 (t70) cc_final: 0.8590 (t0) REVERT: C 638 LEU cc_start: 0.9206 (tt) cc_final: 0.8913 (tt) REVERT: C 763 MET cc_start: 0.9308 (tpp) cc_final: 0.8948 (tpp) REVERT: C 982 LEU cc_start: 0.9733 (OUTLIER) cc_final: 0.9508 (mm) REVERT: C 1118 PHE cc_start: 0.7782 (m-80) cc_final: 0.7445 (m-80) outliers start: 96 outliers final: 61 residues processed: 244 average time/residue: 0.2033 time to fit residues: 81.9083 Evaluate side-chains 219 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 147 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 655 GLN Chi-restraints excluded: chain B residue 761 CYS Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain B residue 1109 LYS Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1130 ARG Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1149 CYS Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 761 CYS Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1109 LYS Chi-restraints excluded: chain C residue 1127 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 428 optimal weight: 0.7980 chunk 355 optimal weight: 5.9990 chunk 303 optimal weight: 5.9990 chunk 362 optimal weight: 4.9990 chunk 413 optimal weight: 3.9990 chunk 361 optimal weight: 7.9990 chunk 358 optimal weight: 2.9990 chunk 256 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 310 optimal weight: 4.9990 chunk 255 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN B 153 GLN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 945 GLN A 149 ASN A 712 GLN ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 GLN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.102417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.058331 restraints weight = 148107.188| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 5.89 r_work: 0.2864 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.137 35211 Z= 0.247 Angle : 0.654 14.931 47940 Z= 0.329 Chirality : 0.044 0.179 5406 Planarity : 0.004 0.057 6174 Dihedral : 5.159 50.672 4834 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.06 % Favored : 89.85 % Rotamer: Outliers : 2.46 % Allowed : 12.89 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.12), residues: 4392 helix: 1.82 (0.20), residues: 734 sheet: -1.02 (0.17), residues: 979 loop : -2.61 (0.11), residues: 2679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 66 TYR 0.034 0.001 TYR A 927 PHE 0.031 0.002 PHE A1118 TRP 0.015 0.001 TRP A 909 HIS 0.006 0.001 HIS C1071 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.25 (35157) covalent geometry : angle 0.65386 / 0.33 (47832) SS BOND : bond 0.00338 / 0.21 ( 54) SS BOND : angle 0.70458 / 0.43 ( 108) hydrogen bonds : bond 0.03643 / 2.39 ( 879) hydrogen bonds : angle 4.81384 / 3.22 ( 2436) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 143 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 29 ILE cc_start: 0.3677 (OUTLIER) cc_final: 0.3138 (pt) REVERT: G 73 ASP cc_start: 0.8762 (m-30) cc_final: 0.8538 (m-30) REVERT: F 35 TRP cc_start: 0.7234 (OUTLIER) cc_final: 0.6404 (t-100) REVERT: I 92 MET cc_start: 0.4737 (ppp) cc_final: 0.4453 (ppp) REVERT: B 866 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7786 (p0) REVERT: B 1109 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8933 (pttm) REVERT: A 148 MET cc_start: 0.8525 (mmp) cc_final: 0.7315 (ttp) REVERT: A 192 MET cc_start: 0.4560 (mmt) cc_final: 0.4076 (mmt) REVERT: A 400 THR cc_start: 0.5242 (OUTLIER) cc_final: 0.5011 (m) REVERT: A 598 ASP cc_start: 0.9343 (t0) cc_final: 0.9045 (t0) REVERT: A 952 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.9201 (tppt) REVERT: C 235 LEU cc_start: 0.9684 (tp) cc_final: 0.9366 (tt) REVERT: C 297 TYR cc_start: 0.8698 (m-80) cc_final: 0.8187 (m-80) REVERT: C 638 LEU cc_start: 0.9482 (tt) cc_final: 0.9215 (tt) REVERT: C 655 GLN cc_start: 0.9444 (OUTLIER) cc_final: 0.9215 (mm110) REVERT: C 763 MET cc_start: 0.9553 (tpp) cc_final: 0.9235 (tpp) REVERT: C 982 LEU cc_start: 0.9790 (OUTLIER) cc_final: 0.9570 (mm) outliers start: 94 outliers final: 70 residues processed: 230 average time/residue: 0.1999 time to fit residues: 75.5379 Evaluate side-chains 210 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 132 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 148 GLN Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 757 THR Chi-restraints excluded: chain B residue 761 CYS Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain B residue 1109 LYS Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1130 ARG Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain A residue 142 TRP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 655 GLN Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 761 CYS Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1109 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 351 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 31 optimal weight: 40.0000 chunk 265 optimal weight: 30.0000 chunk 162 optimal weight: 7.9990 chunk 371 optimal weight: 8.9990 chunk 267 optimal weight: 20.0000 chunk 405 optimal weight: 0.8980 chunk 315 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 387 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.116646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.079919 restraints weight = 189866.280| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 7.38 r_work: 0.2953 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35211 Z= 0.111 Angle : 0.599 14.430 47940 Z= 0.296 Chirality : 0.043 0.178 5406 Planarity : 0.004 0.058 6174 Dihedral : 5.006 48.541 4830 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.95 % Favored : 90.98 % Rotamer: Outliers : 1.99 % Allowed : 13.57 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.13), residues: 4392 helix: 1.96 (0.20), residues: 732 sheet: -0.99 (0.16), residues: 1065 loop : -2.51 (0.11), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 66 TYR 0.014 0.001 TYR A 639 PHE 0.037 0.001 PHE A 124 TRP 0.017 0.001 TRP B 909 HIS 0.003 0.000 HIS C1071 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (35157) covalent geometry : angle 0.59827 / 0.30 (47832) SS BOND : bond 0.00222 / 0.12 ( 54) SS BOND : angle 0.71108 / 0.43 ( 108) hydrogen bonds : bond 0.03172 / 2.07 ( 879) hydrogen bonds : angle 4.59510 / 3.09 ( 2436) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 142 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 29 ILE cc_start: 0.3101 (OUTLIER) cc_final: 0.2557 (pt) REVERT: G 73 ASP cc_start: 0.8603 (m-30) cc_final: 0.8379 (m-30) REVERT: F 35 TRP cc_start: 0.7142 (OUTLIER) cc_final: 0.6289 (t-100) REVERT: F 47 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8365 (tm) REVERT: I 92 MET cc_start: 0.4438 (ppp) cc_final: 0.4119 (ppp) REVERT: B 148 MET cc_start: 0.7945 (mmt) cc_final: 0.7451 (mmm) REVERT: B 866 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7839 (p0) REVERT: B 927 TYR cc_start: 0.9201 (t80) cc_final: 0.8928 (t80) REVERT: B 1109 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8818 (pttm) REVERT: B 1130 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8236 (tpp80) REVERT: A 192 MET cc_start: 0.4463 (mmt) cc_final: 0.4068 (mmt) REVERT: A 400 THR cc_start: 0.5041 (OUTLIER) cc_final: 0.4808 (m) REVERT: A 598 ASP cc_start: 0.9285 (t0) cc_final: 0.8961 (t0) REVERT: A 892 MET cc_start: 0.9717 (mtt) cc_final: 0.9458 (mtt) REVERT: A 1064 ASP cc_start: 0.9143 (t0) cc_final: 0.8870 (t0) REVERT: C 235 LEU cc_start: 0.9646 (tp) cc_final: 0.9334 (tt) REVERT: C 297 TYR cc_start: 0.8537 (m-80) cc_final: 0.8039 (m-80) REVERT: C 638 LEU cc_start: 0.9388 (tt) cc_final: 0.9071 (tt) REVERT: C 763 MET cc_start: 0.9566 (tpp) cc_final: 0.9232 (tpp) REVERT: C 982 LEU cc_start: 0.9766 (OUTLIER) cc_final: 0.9520 (mm) outliers start: 76 outliers final: 60 residues processed: 215 average time/residue: 0.2118 time to fit residues: 75.2088 Evaluate side-chains 207 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 139 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 761 CYS Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain B residue 1109 LYS Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1130 ARG Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 761 CYS Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1109 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 305 optimal weight: 20.0000 chunk 133 optimal weight: 0.6980 chunk 312 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 71 optimal weight: 50.0000 chunk 22 optimal weight: 20.0000 chunk 118 optimal weight: 50.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 ASN C 733 ASN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.101592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.056958 restraints weight = 147046.531| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 5.83 r_work: 0.2831 rms_B_bonded: 5.74 restraints_weight: 2.0000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 35211 Z= 0.285 Angle : 0.699 14.693 47940 Z= 0.354 Chirality : 0.045 0.193 5406 Planarity : 0.004 0.060 6174 Dihedral : 5.359 50.240 4826 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.91 % Favored : 88.98 % Rotamer: Outliers : 2.04 % Allowed : 13.46 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.13), residues: 4392 helix: 1.62 (0.20), residues: 739 sheet: -0.95 (0.17), residues: 966 loop : -2.50 (0.11), residues: 2687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 66 TYR 0.024 0.001 TYR A 293 PHE 0.036 0.002 PHE A 124 TRP 0.016 0.001 TRP A 909 HIS 0.006 0.001 HIS C1071 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.28 (35157) covalent geometry : angle 0.69855 / 0.35 (47832) SS BOND : bond 0.00416 / 0.26 ( 54) SS BOND : angle 0.87013 / 0.52 ( 108) hydrogen bonds : bond 0.03881 / 2.55 ( 879) hydrogen bonds : angle 4.96927 / 3.33 ( 2436) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14948.02 seconds wall clock time: 254 minutes 3.82 seconds (15243.82 seconds total)