Starting phenix.real_space_refine on Sun Jun 29 16:28:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kds_37144/06_2025/8kds_37144.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kds_37144/06_2025/8kds_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8kds_37144/06_2025/8kds_37144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kds_37144/06_2025/8kds_37144.map" model { file = "/net/cci-nas-00/data/ceres_data/8kds_37144/06_2025/8kds_37144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kds_37144/06_2025/8kds_37144.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.82s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 20.55, per 1000 atoms: 0.60 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: 8.50 Conformation dependent library (CDL) restraints added in 4.5 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: 4.85 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: 13.35 Time building geometry restraints manager: 10.06 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: 0.02 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: 1.630 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: 0.030 Extract box with map and model: 1.390 Check model and map are aligned: 0.290 Set scattering table: 0.400 Process input model: 77.060 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (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 TRP 0.006 0.000 TRP A 464 HIS 0.003 0.000 HIS C1071 PHE 0.008 0.001 PHE B 357 TYR 0.004 0.000 TYR D 141 ARG 0.002 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.21314 ( 879) hydrogen bonds : angle 8.20286 ( 2436) SS BOND : bond 0.00131 ( 54) SS BOND : angle 0.53052 ( 108) covalent geometry : bond 0.00286 (35157) covalent geometry : angle 0.51078 (47832) *********************** 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 : 4.933 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: 0.5718 (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: 0.7283 time to fit residues: 667.2947 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 : 6.161 ------------------------------------------------------------------------------- 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 372 optimal weight: 40.0000 chunk 334 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 chunk 114 optimal weight: 50.0000 chunk 225 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 345 optimal weight: 0.3980 chunk 133 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 chunk 257 optimal weight: 30.0000 chunk 400 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** H 34 ASN H 89 GLN H 101 GLN H 148 GLN B 149 ASN B 153 GLN B 242 GLN B 362 ASN B 437 GLN B 546 ASN B 564 GLN B 587 GLN B 591 GLN B 673 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 587 GLN 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 119 ASN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN C 587 GLN C 824 ASN C 876 GLN C 937 ASN C1077 GLN 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 = 0.4353 r_free = 0.4353 target = 0.108733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.067999 restraints weight = 148605.382| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 5.97 r_work: 0.3213 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2185 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= 0.147 Angle : 0.574 9.451 47940 Z= 0.290 Chirality : 0.043 0.209 5406 Planarity : 0.004 0.064 6174 Dihedral : 5.470 79.179 4892 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.27 % Favored : 91.67 % Rotamer: Outliers : 3.42 % Allowed : 9.80 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.12), residues: 4392 helix: 1.78 (0.20), residues: 685 sheet: -2.15 (0.14), residues: 1142 loop : -3.46 (0.10), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 35 HIS 0.003 0.001 HIS C1081 PHE 0.031 0.001 PHE A 124 TYR 0.026 0.001 TYR I 108 ARG 0.011 0.000 ARG A1130 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 879) hydrogen bonds : angle 5.81917 ( 2436) SS BOND : bond 0.00198 ( 54) SS BOND : angle 0.84984 ( 108) covalent geometry : bond 0.00330 (35157) covalent geometry : angle 0.57349 (47832) *********************** 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 312 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 181 time to evaluate : 4.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 67 PHE cc_start: 0.2185 (m-80) cc_final: 0.1818 (m-80) REVERT: F 35 TRP cc_start: 0.7391 (OUTLIER) cc_final: 0.6492 (t-100) REVERT: B 192 MET cc_start: 0.5577 (mmt) cc_final: 0.4766 (mmt) REVERT: B 293 TYR cc_start: 0.7926 (m-10) cc_final: 0.7662 (m-10) REVERT: B 438 ILE cc_start: 0.2617 (OUTLIER) cc_final: 0.2351 (mm) REVERT: B 866 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7546 (p0) REVERT: B 892 MET cc_start: 0.9708 (mtt) cc_final: 0.9387 (mtm) REVERT: B 989 LEU cc_start: 0.9344 (tt) cc_final: 0.9109 (tt) REVERT: B 1109 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8830 (ptpp) REVERT: B 1149 CYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7955 (m) REVERT: A 192 MET cc_start: 0.4566 (mmt) cc_final: 0.4074 (mmt) REVERT: A 400 THR cc_start: 0.5475 (OUTLIER) cc_final: 0.5182 (m) REVERT: A 598 ASP cc_start: 0.8861 (t0) cc_final: 0.8615 (t0) REVERT: A 712 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7929 (pp30) REVERT: A 856 PHE cc_start: 0.8546 (m-10) cc_final: 0.8346 (m-80) REVERT: A 952 LYS cc_start: 0.9488 (OUTLIER) cc_final: 0.9167 (tppt) REVERT: A 1064 ASP cc_start: 0.8660 (t0) cc_final: 0.8431 (t0) REVERT: A 1149 CYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8238 (m) REVERT: C 235 LEU cc_start: 0.9548 (tp) cc_final: 0.9280 (tt) REVERT: C 361 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8201 (p) outliers start: 131 outliers final: 53 residues processed: 300 average time/residue: 0.4789 time to fit residues: 234.3093 Evaluate side-chains 214 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 151 time to evaluate : 3.875 ------------------------------------------------------------------------------- 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 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 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 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 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 715 ILE 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 712 GLN Chi-restraints excluded: chain A residue 757 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 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 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 383 optimal weight: 0.9980 chunk 308 optimal weight: 2.9990 chunk 156 optimal weight: 20.0000 chunk 296 optimal weight: 0.4980 chunk 264 optimal weight: 5.9990 chunk 8 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 305 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 37 HIS F 125 GLN I 171 HIS B 119 ASN B 520 ASN B 564 GLN ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 937 ASN B 983 ASN A 196 ASN A 437 GLN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 HIS ** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN A 945 GLN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN C 640 GLN C 673 GLN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.104709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.061469 restraints weight = 146870.833| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 5.94 r_work: 0.2963 rms_B_bonded: 5.14 restraints_weight: 2.0000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 35211 Z= 0.250 Angle : 0.643 10.197 47940 Z= 0.328 Chirality : 0.044 0.239 5406 Planarity : 0.004 0.061 6174 Dihedral : 5.237 71.252 4848 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.20 % Favored : 90.71 % Rotamer: Outliers : 3.50 % Allowed : 9.62 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.12), residues: 4392 helix: 1.83 (0.20), residues: 683 sheet: -1.84 (0.15), residues: 1038 loop : -3.25 (0.10), residues: 2671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 909 HIS 0.011 0.001 HIS A1071 PHE 0.033 0.002 PHE C 124 TYR 0.019 0.001 TYR A 927 ARG 0.025 0.001 ARG B1130 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 879) hydrogen bonds : angle 5.40568 ( 2436) SS BOND : bond 0.00787 ( 54) SS BOND : angle 0.88189 ( 108) covalent geometry : bond 0.00562 (35157) covalent geometry : angle 0.64258 (47832) *********************** 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 297 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 163 time to evaluate : 3.786 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: G 73 ASP cc_start: 0.8674 (m-30) cc_final: 0.8391 (m-30) REVERT: G 82 MET cc_start: 0.0921 (mmm) cc_final: 0.0185 (mmt) REVERT: F 24 ARG cc_start: 0.9328 (mtm110) cc_final: 0.8896 (ptt-90) REVERT: F 35 TRP cc_start: 0.7452 (OUTLIER) cc_final: 0.6673 (t-100) REVERT: B 231 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9255 (pttp) REVERT: B 438 ILE cc_start: 0.2610 (OUTLIER) cc_final: 0.2338 (mm) REVERT: B 763 MET cc_start: 0.9670 (tpp) cc_final: 0.8993 (tpp) REVERT: B 866 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7674 (p0) REVERT: B 1109 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8878 (pttm) REVERT: A 192 MET cc_start: 0.4527 (mmt) cc_final: 0.4069 (mmt) REVERT: A 400 THR cc_start: 0.5450 (OUTLIER) cc_final: 0.5180 (m) REVERT: A 598 ASP cc_start: 0.9130 (t0) cc_final: 0.8887 (t0) REVERT: A 642 VAL cc_start: 0.9436 (OUTLIER) cc_final: 0.9200 (m) REVERT: A 671 GLN cc_start: 0.7551 (mp10) cc_final: 0.7283 (mp10) REVERT: A 712 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7815 (pp30) REVERT: A 754 MET cc_start: 0.9477 (ptm) cc_final: 0.9203 (ptp) REVERT: A 952 LYS cc_start: 0.9525 (OUTLIER) cc_final: 0.9258 (tppt) REVERT: A 1064 ASP cc_start: 0.9059 (t0) cc_final: 0.8653 (t0) REVERT: C 297 TYR cc_start: 0.8656 (m-80) cc_final: 0.8153 (m-80) REVERT: C 857 MET cc_start: 0.9221 (tmm) cc_final: 0.9019 (tmm) REVERT: C 1127 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.7975 (mt) outliers start: 134 outliers final: 78 residues processed: 284 average time/residue: 0.4586 time to fit residues: 216.2112 Evaluate side-chains 228 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 140 time to evaluate : 4.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 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 E residue 214 VAL 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 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 156 ILE Chi-restraints excluded: chain B residue 193 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 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 613 ASP Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 676 CYS 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 925 MET Chi-restraints excluded: chain B residue 983 ASN Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1109 LYS Chi-restraints excluded: chain B residue 1127 ILE 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 263 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 496 ILE 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 757 THR Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 849 VAL 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 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 613 ASP Chi-restraints excluded: chain C residue 614 ILE 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 1109 LYS Chi-restraints excluded: chain C residue 1127 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 126 optimal weight: 1.9990 chunk 124 optimal weight: 50.0000 chunk 278 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 54 optimal weight: 40.0000 chunk 218 optimal weight: 0.8980 chunk 153 optimal weight: 20.0000 chunk 37 optimal weight: 50.0000 chunk 47 optimal weight: 30.0000 chunk 127 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 38 GLN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.104686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.062072 restraints weight = 145977.652| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 6.04 r_work: 0.2963 rms_B_bonded: 5.12 restraints_weight: 2.0000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 35211 Z= 0.198 Angle : 0.593 10.095 47940 Z= 0.301 Chirality : 0.043 0.195 5406 Planarity : 0.004 0.060 6174 Dihedral : 5.143 62.042 4842 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.81 % Favored : 91.10 % Rotamer: Outliers : 3.24 % Allowed : 10.30 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.12), residues: 4392 helix: 1.82 (0.20), residues: 708 sheet: -1.76 (0.15), residues: 1095 loop : -3.07 (0.10), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 464 HIS 0.005 0.001 HIS A1071 PHE 0.025 0.001 PHE A 124 TYR 0.015 0.001 TYR C 293 ARG 0.009 0.000 ARG B1062 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 879) hydrogen bonds : angle 5.11111 ( 2436) SS BOND : bond 0.00281 ( 54) SS BOND : angle 0.86553 ( 108) covalent geometry : bond 0.00448 (35157) covalent geometry : angle 0.59181 (47832) *********************** 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 278 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 154 time to evaluate : 4.082 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: 0.8711 (m-30) cc_final: 0.8464 (m-30) REVERT: G 82 MET cc_start: 0.0571 (mmm) cc_final: -0.0080 (mmt) REVERT: F 24 ARG cc_start: 0.9361 (mtm110) cc_final: 0.8990 (ptt-90) REVERT: F 35 TRP cc_start: 0.7359 (OUTLIER) cc_final: 0.6610 (t-100) REVERT: B 101 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8724 (tm) REVERT: B 142 TRP cc_start: 0.8760 (m-90) cc_final: 0.8494 (m-90) REVERT: B 148 MET cc_start: 0.7424 (mmt) cc_final: 0.7041 (mmm) REVERT: B 231 LYS cc_start: 0.9471 (OUTLIER) cc_final: 0.9226 (pttp) REVERT: B 438 ILE cc_start: 0.2501 (OUTLIER) cc_final: 0.2197 (mm) REVERT: B 866 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7782 (p0) REVERT: B 1149 CYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8111 (m) REVERT: A 101 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9011 (tm) REVERT: A 148 MET cc_start: 0.8418 (mmp) cc_final: 0.6854 (ttt) REVERT: A 192 MET cc_start: 0.4483 (mmt) cc_final: 0.4034 (mmt) REVERT: A 400 THR cc_start: 0.5535 (OUTLIER) cc_final: 0.5283 (m) REVERT: A 598 ASP cc_start: 0.9185 (t0) cc_final: 0.8888 (t0) REVERT: A 642 VAL cc_start: 0.9444 (OUTLIER) cc_final: 0.9227 (m) REVERT: A 712 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7917 (pp30) REVERT: A 952 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.9231 (tppt) REVERT: A 1064 ASP cc_start: 0.9022 (t0) cc_final: 0.8566 (t0) REVERT: A 1118 PHE cc_start: 0.7130 (m-80) cc_final: 0.6923 (m-80) REVERT: C 235 LEU cc_start: 0.9653 (tp) cc_final: 0.9322 (tt) REVERT: C 263 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8145 (pt) REVERT: C 361 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8375 (p) REVERT: C 598 ASP cc_start: 0.9317 (t0) cc_final: 0.8636 (t0) REVERT: C 892 MET cc_start: 0.9603 (mtm) cc_final: 0.9240 (mtm) REVERT: C 1052 MET cc_start: 0.9670 (tpp) cc_final: 0.9425 (tpp) REVERT: C 1074 SER cc_start: 0.9254 (t) cc_final: 0.8982 (p) outliers start: 124 outliers final: 72 residues processed: 267 average time/residue: 0.4769 time to fit residues: 211.1944 Evaluate side-chains 232 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 147 time to evaluate : 4.102 ------------------------------------------------------------------------------- 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 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 107 ILE Chi-restraints excluded: chain I residue 40 THR 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 101 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 231 LYS 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 438 ILE 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 613 ASP 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 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 101 LEU Chi-restraints excluded: chain A residue 128 ILE 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 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 782 PHE Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 849 VAL 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 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 263 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 622 VAL 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 1109 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 110 optimal weight: 40.0000 chunk 379 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 chunk 382 optimal weight: 0.7980 chunk 351 optimal weight: 0.0470 chunk 13 optimal weight: 0.8980 chunk 162 optimal weight: 50.0000 chunk 338 optimal weight: 6.9990 chunk 378 optimal weight: 30.0000 chunk 42 optimal weight: 40.0000 chunk 102 optimal weight: 7.9990 overall best weight: 2.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 HIS ** 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 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 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 ** C1077 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 = 0.4254 r_free = 0.4254 target = 0.104011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.061129 restraints weight = 145147.584| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 6.11 r_work: 0.2932 rms_B_bonded: 5.71 restraints_weight: 2.0000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 35211 Z= 0.187 Angle : 0.594 13.017 47940 Z= 0.300 Chirality : 0.043 0.189 5406 Planarity : 0.004 0.060 6174 Dihedral : 5.170 54.504 4842 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.63 % Favored : 90.28 % Rotamer: Outliers : 3.45 % Allowed : 10.67 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.12), residues: 4392 helix: 1.67 (0.20), residues: 740 sheet: -1.45 (0.15), residues: 1062 loop : -2.98 (0.11), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 464 HIS 0.006 0.001 HIS C1071 PHE 0.031 0.001 PHE B1120 TYR 0.027 0.001 TYR A 927 ARG 0.005 0.000 ARG E 66 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 879) hydrogen bonds : angle 4.89010 ( 2436) SS BOND : bond 0.00269 ( 54) SS BOND : angle 0.70231 ( 108) covalent geometry : bond 0.00422 (35157) covalent geometry : angle 0.59371 (47832) *********************** 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 287 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 155 time to evaluate : 3.898 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: 0.8670 (m-30) cc_final: 0.8368 (m-30) REVERT: G 82 MET cc_start: 0.0630 (mmm) cc_final: 0.0285 (mmt) REVERT: F 24 ARG cc_start: 0.9371 (mtm110) cc_final: 0.9007 (ptt-90) REVERT: F 35 TRP cc_start: 0.7394 (OUTLIER) cc_final: 0.6604 (t-100) REVERT: B 101 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8825 (tm) REVERT: B 148 MET cc_start: 0.7864 (mmt) cc_final: 0.7480 (mmm) REVERT: B 293 TYR cc_start: 0.7954 (m-10) cc_final: 0.7543 (m-10) REVERT: B 866 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7684 (p0) REVERT: B 892 MET cc_start: 0.9704 (mtt) cc_final: 0.9333 (mtm) REVERT: A 101 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9069 (tm) REVERT: A 192 MET cc_start: 0.4554 (mmt) cc_final: 0.4067 (mmt) REVERT: A 400 THR cc_start: 0.5493 (OUTLIER) cc_final: 0.5241 (m) REVERT: A 598 ASP cc_start: 0.9226 (t0) cc_final: 0.8924 (t0) REVERT: A 712 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7922 (pp30) REVERT: A 952 LYS cc_start: 0.9496 (OUTLIER) cc_final: 0.9186 (tppt) REVERT: A 1064 ASP cc_start: 0.9163 (t0) cc_final: 0.8823 (t0) REVERT: A 1118 PHE cc_start: 0.7151 (m-80) cc_final: 0.6934 (m-80) REVERT: C 192 MET cc_start: 0.5510 (mmt) cc_final: 0.5307 (mmt) REVERT: C 235 LEU cc_start: 0.9648 (tp) cc_final: 0.9349 (tt) REVERT: C 598 ASP cc_start: 0.9381 (t0) cc_final: 0.8671 (t0) REVERT: C 673 GLN cc_start: 0.9129 (tp-100) cc_final: 0.8915 (tp-100) REVERT: C 853 ASP cc_start: 0.9092 (OUTLIER) cc_final: 0.8679 (t70) REVERT: C 1052 MET cc_start: 0.9655 (tpp) cc_final: 0.9399 (tpp) REVERT: C 1118 PHE cc_start: 0.8419 (m-80) cc_final: 0.8217 (m-80) outliers start: 132 outliers final: 81 residues processed: 275 average time/residue: 0.4655 time to fit residues: 214.4864 Evaluate side-chains 231 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 142 time to evaluate : 3.756 ------------------------------------------------------------------------------- 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 95 CYS Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain D residue 28 THR 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 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 H residue 106 GLU Chi-restraints excluded: chain B residue 101 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 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 613 ASP 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 982 LEU 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 1152 VAL Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain A residue 101 LEU 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 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 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 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 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 853 ASP Chi-restraints excluded: chain C residue 873 ILE 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 134 optimal weight: 0.0000 chunk 147 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 331 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 191 optimal weight: 0.9990 chunk 40 optimal weight: 50.0000 chunk 179 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 319 optimal weight: 0.7980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 HIS ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 945 GLN ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.104989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.063257 restraints weight = 152706.864| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 5.45 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35211 Z= 0.111 Angle : 0.566 12.941 47940 Z= 0.282 Chirality : 0.043 0.189 5406 Planarity : 0.004 0.059 6174 Dihedral : 5.022 53.106 4840 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.81 % Favored : 91.12 % Rotamer: Outliers : 2.88 % Allowed : 11.61 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.12), residues: 4392 helix: 1.97 (0.20), residues: 729 sheet: -1.24 (0.16), residues: 1026 loop : -2.85 (0.11), residues: 2637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 464 HIS 0.003 0.000 HIS B1087 PHE 0.040 0.001 PHE B1120 TYR 0.014 0.001 TYR C 639 ARG 0.005 0.000 ARG C 870 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 879) hydrogen bonds : angle 4.64836 ( 2436) SS BOND : bond 0.00215 ( 54) SS BOND : angle 0.71700 ( 108) covalent geometry : bond 0.00257 (35157) covalent geometry : angle 0.56520 (47832) *********************** 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 261 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 151 time to evaluate : 3.758 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: 0.8503 (m-30) cc_final: 0.8183 (m-30) REVERT: F 35 TRP cc_start: 0.7307 (OUTLIER) cc_final: 0.6502 (t-100) REVERT: B 148 MET cc_start: 0.7786 (mmt) cc_final: 0.7474 (mmm) REVERT: B 655 GLN cc_start: 0.9404 (OUTLIER) cc_final: 0.9019 (mm110) REVERT: B 866 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7743 (p0) REVERT: A 101 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8932 (tm) REVERT: A 148 MET cc_start: 0.8574 (mmp) cc_final: 0.7189 (ttt) REVERT: A 192 MET cc_start: 0.4203 (mmt) cc_final: 0.3937 (mmt) REVERT: A 400 THR cc_start: 0.5687 (OUTLIER) cc_final: 0.5416 (m) REVERT: A 598 ASP cc_start: 0.8985 (t0) cc_final: 0.8649 (t0) REVERT: A 712 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8079 (pp30) REVERT: A 952 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.9137 (tppt) REVERT: A 1064 ASP cc_start: 0.8711 (t0) cc_final: 0.8345 (t0) REVERT: A 1118 PHE cc_start: 0.6585 (m-80) cc_final: 0.6284 (m-80) REVERT: A 1149 CYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7867 (m) REVERT: C 235 LEU cc_start: 0.9627 (tp) cc_final: 0.9366 (tt) REVERT: C 297 TYR cc_start: 0.7965 (m-80) cc_final: 0.7434 (m-80) REVERT: C 598 ASP cc_start: 0.9188 (t0) cc_final: 0.8466 (t0) REVERT: C 673 GLN cc_start: 0.8994 (tp-100) cc_final: 0.8775 (tp-100) REVERT: C 892 MET cc_start: 0.9462 (mtm) cc_final: 0.9039 (mtm) REVERT: C 1052 MET cc_start: 0.9409 (tpp) cc_final: 0.9116 (tpp) REVERT: C 1118 PHE cc_start: 0.8028 (m-80) cc_final: 0.7618 (m-80) outliers start: 110 outliers final: 75 residues processed: 248 average time/residue: 0.4575 time to fit residues: 188.2244 Evaluate side-chains 227 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 144 time to evaluate : 3.727 ------------------------------------------------------------------------------- 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 95 CYS 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 96 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 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 275 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 655 GLN Chi-restraints excluded: chain B residue 761 CYS Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 1109 LYS Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain A residue 101 LEU 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 364 CYS 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 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 782 PHE 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 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 446 ILE Chi-restraints excluded: chain C residue 622 VAL 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 867 ILE 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 323 optimal weight: 5.9990 chunk 45 optimal weight: 40.0000 chunk 166 optimal weight: 2.9990 chunk 313 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 399 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 326 optimal weight: 0.7980 chunk 316 optimal weight: 3.9990 chunk 403 optimal weight: 2.9990 chunk 247 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 945 GLN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 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 ** C1077 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 = 0.4249 r_free = 0.4249 target = 0.103948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.061353 restraints weight = 148306.209| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 5.64 r_work: 0.2948 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35211 Z= 0.163 Angle : 0.581 14.134 47940 Z= 0.291 Chirality : 0.043 0.181 5406 Planarity : 0.004 0.057 6174 Dihedral : 5.015 53.113 4837 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.43 % Favored : 90.51 % Rotamer: Outliers : 2.93 % Allowed : 12.08 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.12), residues: 4392 helix: 1.95 (0.20), residues: 728 sheet: -1.08 (0.17), residues: 987 loop : -2.79 (0.11), residues: 2677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 464 HIS 0.003 0.001 HIS C1071 PHE 0.028 0.001 PHE A 124 TYR 0.014 0.001 TYR C 293 ARG 0.005 0.000 ARG E 66 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 879) hydrogen bonds : angle 4.66648 ( 2436) SS BOND : bond 0.00256 ( 54) SS BOND : angle 0.69035 ( 108) covalent geometry : bond 0.00373 (35157) covalent geometry : angle 0.58088 (47832) *********************** 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 262 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 150 time to evaluate : 3.909 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: G 73 ASP cc_start: 0.8611 (m-30) cc_final: 0.8342 (m-30) REVERT: G 82 MET cc_start: 0.0792 (mmt) cc_final: 0.0330 (mmp) REVERT: F 35 TRP cc_start: 0.7402 (OUTLIER) cc_final: 0.6520 (t-100) REVERT: I 92 MET cc_start: 0.4096 (ppp) cc_final: 0.3863 (ppp) REVERT: B 148 MET cc_start: 0.8087 (mmt) cc_final: 0.7642 (mmm) REVERT: B 304 MET cc_start: 0.9299 (ttm) cc_final: 0.9098 (ttm) REVERT: B 866 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7849 (p0) REVERT: B 892 MET cc_start: 0.9696 (mtt) cc_final: 0.9371 (mtm) REVERT: B 1073 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8501 (ttp) REVERT: A 101 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9054 (tm) REVERT: A 148 MET cc_start: 0.8558 (mmp) cc_final: 0.7305 (ttt) REVERT: A 192 MET cc_start: 0.4445 (mmt) cc_final: 0.4046 (mmt) REVERT: A 378 VAL cc_start: 0.1867 (OUTLIER) cc_final: 0.1631 (m) REVERT: A 400 THR cc_start: 0.5477 (OUTLIER) cc_final: 0.5228 (m) REVERT: A 598 ASP cc_start: 0.9269 (t0) cc_final: 0.8944 (t0) REVERT: A 712 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7912 (pp30) REVERT: A 1064 ASP cc_start: 0.9120 (t0) cc_final: 0.8802 (t0) REVERT: A 1118 PHE cc_start: 0.7271 (m-80) cc_final: 0.6931 (m-80) REVERT: A 1149 CYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8463 (m) REVERT: C 235 LEU cc_start: 0.9626 (tp) cc_final: 0.9296 (tt) REVERT: C 297 TYR cc_start: 0.8459 (m-80) cc_final: 0.7866 (m-80) REVERT: C 598 ASP cc_start: 0.9401 (t0) cc_final: 0.8794 (t0) REVERT: C 673 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8831 (tp-100) REVERT: C 853 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8491 (t70) REVERT: C 1118 PHE cc_start: 0.8344 (m-80) cc_final: 0.8033 (m-80) outliers start: 112 outliers final: 79 residues processed: 253 average time/residue: 0.4636 time to fit residues: 193.2766 Evaluate side-chains 232 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 144 time to evaluate : 3.805 ------------------------------------------------------------------------------- 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 95 CYS 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 96 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 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 275 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 1159 THR Chi-restraints excluded: chain A residue 101 LEU 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 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 603 VAL 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 770 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 849 VAL 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 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 622 VAL 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 853 ASP Chi-restraints excluded: chain C residue 867 ILE 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 375 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 119 optimal weight: 50.0000 chunk 352 optimal weight: 0.8980 chunk 250 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 282 optimal weight: 8.9990 chunk 289 optimal weight: 5.9990 chunk 45 optimal weight: 50.0000 chunk 361 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 GLN B 153 GLN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 GLN A 149 ASN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 ASN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.102735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.059344 restraints weight = 145843.437| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 5.88 r_work: 0.2882 rms_B_bonded: 5.76 restraints_weight: 2.0000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 35211 Z= 0.225 Angle : 0.633 15.196 47940 Z= 0.319 Chirality : 0.044 0.262 5406 Planarity : 0.004 0.067 6174 Dihedral : 5.218 52.833 4833 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.04 % Favored : 89.87 % Rotamer: Outliers : 2.90 % Allowed : 12.34 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.12), residues: 4392 helix: 1.82 (0.20), residues: 731 sheet: -1.05 (0.17), residues: 988 loop : -2.74 (0.11), residues: 2673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 909 HIS 0.007 0.001 HIS A1071 PHE 0.033 0.002 PHE B1120 TYR 0.018 0.001 TYR A 293 ARG 0.015 0.001 ARG E 66 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 879) hydrogen bonds : angle 4.81736 ( 2436) SS BOND : bond 0.00323 ( 54) SS BOND : angle 0.77501 ( 108) covalent geometry : bond 0.00508 (35157) covalent geometry : angle 0.63270 (47832) *********************** 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 250 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 139 time to evaluate : 3.618 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: G 73 ASP cc_start: 0.8713 (m-30) cc_final: 0.8441 (m-30) REVERT: G 82 MET cc_start: 0.0923 (mmt) cc_final: 0.0399 (mmp) REVERT: F 35 TRP cc_start: 0.7229 (OUTLIER) cc_final: 0.6429 (t-100) REVERT: B 148 MET cc_start: 0.8185 (mmt) cc_final: 0.7720 (mmm) REVERT: B 866 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7778 (p0) REVERT: A 101 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9043 (tm) REVERT: A 192 MET cc_start: 0.4403 (mmt) cc_final: 0.3965 (mmt) REVERT: A 400 THR cc_start: 0.5541 (OUTLIER) cc_final: 0.5307 (m) REVERT: A 598 ASP cc_start: 0.9311 (t0) cc_final: 0.9021 (t0) REVERT: A 712 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7943 (pp30) REVERT: A 1118 PHE cc_start: 0.7329 (m-80) cc_final: 0.7014 (m-80) REVERT: A 1149 CYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8504 (m) REVERT: C 235 LEU cc_start: 0.9696 (tp) cc_final: 0.9402 (tt) REVERT: C 598 ASP cc_start: 0.9426 (t0) cc_final: 0.8866 (t0) REVERT: C 673 GLN cc_start: 0.9200 (tp-100) cc_final: 0.8905 (tp-100) REVERT: C 763 MET cc_start: 0.9531 (tpp) cc_final: 0.9252 (tpp) REVERT: C 853 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8576 (t70) REVERT: C 1118 PHE cc_start: 0.8444 (m-80) cc_final: 0.8113 (m-80) outliers start: 111 outliers final: 78 residues processed: 240 average time/residue: 0.4576 time to fit residues: 185.7315 Evaluate side-chains 223 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 138 time to evaluate : 3.591 ------------------------------------------------------------------------------- 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 95 CYS 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 28 THR 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 96 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 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 275 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 608 THR Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 612 LEU 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 765 ILE 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 1159 THR Chi-restraints excluded: chain A residue 101 LEU 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 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 712 GLN Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 814 THR 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 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 853 ASP Chi-restraints excluded: chain C residue 867 ILE Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 1109 LYS Chi-restraints excluded: chain C residue 1123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 275 optimal weight: 8.9990 chunk 364 optimal weight: 0.0980 chunk 257 optimal weight: 30.0000 chunk 12 optimal weight: 50.0000 chunk 24 optimal weight: 40.0000 chunk 35 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 291 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 60 optimal weight: 30.0000 chunk 388 optimal weight: 1.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 362 ASN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 GLN ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN A 564 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN ** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 GLN C 371 ASN C 733 ASN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1034 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 = 0.4173 r_free = 0.4173 target = 0.100696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.056216 restraints weight = 149192.021| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 5.77 r_work: 0.2797 rms_B_bonded: 5.37 restraints_weight: 2.0000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.139 35211 Z= 0.345 Angle : 0.734 14.775 47940 Z= 0.377 Chirality : 0.046 0.220 5406 Planarity : 0.005 0.073 6174 Dihedral : 5.759 52.354 4829 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.32 % Favored : 88.57 % Rotamer: Outliers : 2.59 % Allowed : 12.71 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.12), residues: 4392 helix: 1.26 (0.19), residues: 751 sheet: -1.09 (0.16), residues: 1003 loop : -2.72 (0.11), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 909 HIS 0.008 0.001 HIS C1071 PHE 0.053 0.002 PHE A1098 TYR 0.030 0.002 TYR A 293 ARG 0.013 0.001 ARG E 66 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 879) hydrogen bonds : angle 5.24445 ( 2436) SS BOND : bond 0.00485 ( 54) SS BOND : angle 1.00981 ( 108) covalent geometry : bond 0.00770 (35157) covalent geometry : angle 0.73362 (47832) *********************** 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 228 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 129 time to evaluate : 3.734 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: G 73 ASP cc_start: 0.8875 (m-30) cc_final: 0.8675 (m-30) REVERT: G 82 MET cc_start: 0.1028 (mmt) cc_final: 0.0474 (mmp) REVERT: I 92 MET cc_start: 0.4924 (ppp) cc_final: 0.4678 (ppp) REVERT: B 866 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7841 (p0) REVERT: A 101 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9251 (tm) REVERT: A 192 MET cc_start: 0.4869 (mmt) cc_final: 0.4386 (mmt) REVERT: A 598 ASP cc_start: 0.9377 (t0) cc_final: 0.9136 (t0) REVERT: A 1115 GLU cc_start: 0.9117 (tp30) cc_final: 0.8874 (tp30) REVERT: A 1118 PHE cc_start: 0.7504 (m-80) cc_final: 0.7232 (m-80) REVERT: C 763 MET cc_start: 0.9546 (tpp) cc_final: 0.9256 (tpp) REVERT: C 853 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8591 (t70) REVERT: C 1118 PHE cc_start: 0.8459 (m-80) cc_final: 0.8209 (m-80) outliers start: 99 outliers final: 81 residues processed: 221 average time/residue: 0.4363 time to fit residues: 162.1003 Evaluate side-chains 208 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 124 time to evaluate : 3.666 ------------------------------------------------------------------------------- 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 67 PHE 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 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 96 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 214 VAL 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 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 275 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 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 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 856 PHE Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 966 THR Chi-restraints excluded: chain B residue 982 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 1159 THR Chi-restraints excluded: chain A residue 101 LEU 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 364 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 580 THR 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 770 THR Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 851 LEU 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 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 622 VAL 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 853 ASP Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 1109 LYS Chi-restraints excluded: chain C residue 1123 THR Chi-restraints excluded: chain C residue 1127 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 424 optimal weight: 2.9990 chunk 389 optimal weight: 3.9990 chunk 32 optimal weight: 0.0020 chunk 127 optimal weight: 0.9980 chunk 331 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 82 optimal weight: 30.0000 chunk 284 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 270 optimal weight: 8.9990 chunk 350 optimal weight: 3.9990 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 178 GLN ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN ** B 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 GLN ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 ASN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 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 = 0.4241 r_free = 0.4241 target = 0.105197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.060948 restraints weight = 172813.279| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 7.48 r_work: 0.2850 rms_B_bonded: 6.54 restraints_weight: 2.0000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35211 Z= 0.150 Angle : 0.626 14.675 47940 Z= 0.314 Chirality : 0.044 0.243 5406 Planarity : 0.004 0.058 6174 Dihedral : 5.415 50.251 4822 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.68 % Favored : 90.23 % Rotamer: Outliers : 2.12 % Allowed : 13.36 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.13), residues: 4392 helix: 1.62 (0.20), residues: 750 sheet: -0.98 (0.17), residues: 952 loop : -2.61 (0.11), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 35 HIS 0.004 0.001 HIS B1071 PHE 0.038 0.001 PHE A 124 TYR 0.012 0.001 TYR B1090 ARG 0.013 0.000 ARG E 66 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 879) hydrogen bonds : angle 4.82697 ( 2436) SS BOND : bond 0.00289 ( 54) SS BOND : angle 0.79249 ( 108) covalent geometry : bond 0.00344 (35157) covalent geometry : angle 0.62577 (47832) ********************** 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 211 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 130 time to evaluate : 3.717 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: B 866 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7801 (p0) REVERT: A 101 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9011 (tm) REVERT: A 192 MET cc_start: 0.4552 (mmt) cc_final: 0.4034 (mmt) REVERT: A 598 ASP cc_start: 0.9352 (t0) cc_final: 0.9048 (t0) REVERT: A 712 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7852 (pp30) REVERT: A 927 TYR cc_start: 0.9249 (t80) cc_final: 0.9044 (t80) REVERT: A 1118 PHE cc_start: 0.7329 (m-80) cc_final: 0.7065 (m-80) REVERT: C 763 MET cc_start: 0.9585 (tpp) cc_final: 0.9271 (tpp) REVERT: C 853 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8506 (t70) REVERT: C 892 MET cc_start: 0.9556 (mtm) cc_final: 0.9321 (mtm) outliers start: 81 outliers final: 71 residues processed: 207 average time/residue: 0.4793 time to fit residues: 167.1478 Evaluate side-chains 198 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 123 time to evaluate : 3.803 ------------------------------------------------------------------------------- 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 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 96 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 214 VAL 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 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 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 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 712 GLN 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 966 THR 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 1159 THR Chi-restraints excluded: chain A residue 101 LEU 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 364 CYS Chi-restraints excluded: chain A residue 389 CYS 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 814 THR 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 158 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 265 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 761 CYS Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 1109 LYS Chi-restraints excluded: chain C residue 1123 THR Chi-restraints excluded: chain C residue 1127 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 327 optimal weight: 4.9990 chunk 231 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 127 optimal weight: 0.2980 chunk 312 optimal weight: 2.9990 chunk 203 optimal weight: 0.6980 chunk 131 optimal weight: 9.9990 chunk 39 optimal weight: 50.0000 chunk 205 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 433 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 HIS B 712 GLN ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4253 r_free = 0.4253 target = 0.105809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.062055 restraints weight = 172798.061| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 7.87 r_work: 0.2889 rms_B_bonded: 5.69 restraints_weight: 2.0000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35211 Z= 0.121 Angle : 0.627 14.650 47940 Z= 0.311 Chirality : 0.043 0.225 5406 Planarity : 0.004 0.058 6174 Dihedral : 5.275 49.915 4822 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.72 % Favored : 90.19 % Rotamer: Outliers : 2.09 % Allowed : 13.57 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 4392 helix: 1.70 (0.20), residues: 753 sheet: -0.83 (0.17), residues: 929 loop : -2.56 (0.11), residues: 2710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 909 HIS 0.003 0.001 HIS B1071 PHE 0.039 0.001 PHE A 124 TYR 0.013 0.001 TYR C1090 ARG 0.015 0.000 ARG E 66 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 879) hydrogen bonds : angle 4.64305 ( 2436) SS BOND : bond 0.00254 ( 54) SS BOND : angle 0.72076 ( 108) covalent geometry : bond 0.00283 (35157) covalent geometry : angle 0.62677 (47832) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41791.47 seconds wall clock time: 715 minutes 57.03 seconds (42957.03 seconds total)