Starting phenix.real_space_refine on Sat Aug 10 07:14:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9b_36983/08_2024/8k9b_36983.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9b_36983/08_2024/8k9b_36983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9b_36983/08_2024/8k9b_36983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9b_36983/08_2024/8k9b_36983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9b_36983/08_2024/8k9b_36983.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9b_36983/08_2024/8k9b_36983.cif" } resolution = 4.5 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= 0.009 sd= 0.093 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 130 5.16 5 C 18105 2.51 5 N 4744 2.21 5 O 5461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 28440 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 8407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8407 Classifications: {'peptide': 1075} Link IDs: {'CIS': 2, 'PTRANS': 53, 'TRANS': 1019} Chain breaks: 4 Chain: "A" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1633 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 201} Chain: "B" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1699 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Chain: "C" Number of atoms: 8332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8332 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 52, 'TRANS': 1012} Chain breaks: 5 Chain: "D" Number of atoms: 8355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8355 Classifications: {'peptide': 1068} Link IDs: {'PTRANS': 52, 'TRANS': 1015} Chain breaks: 5 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 17.58, per 1000 atoms: 0.62 Number of scatterers: 28440 At special positions: 0 Unit cell: (184.62, 184.62, 192.78, 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 130 16.00 O 5461 8.00 N 4744 7.00 C 18105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG E1301 " - " ASN E 122 " Time building additional restraints: 11.30 Conformation dependent library (CDL) restraints added in 5.6 seconds 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6818 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 57 sheets defined 21.7% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.32 Creating SS restraints... Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 383 through 388 removed outlier: 3.610A pdb=" N ASN E 388 " --> pdb=" O PRO E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 408 removed outlier: 4.439A pdb=" N ARG E 408 " --> pdb=" O GLY E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'E' and resid 737 through 744 removed outlier: 3.778A pdb=" N ILE E 742 " --> pdb=" O CYS E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 757 Processing helix chain 'E' and resid 758 through 783 Processing helix chain 'E' and resid 816 through 825 removed outlier: 3.899A pdb=" N LEU E 821 " --> pdb=" O PHE E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 849 through 856 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 913 through 941 removed outlier: 3.688A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN E 925 " --> pdb=" O LYS E 921 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 968 removed outlier: 3.580A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU E 966 " --> pdb=" O LEU E 962 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER E 967 " --> pdb=" O VAL E 963 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E 968 " --> pdb=" O LYS E 964 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1032 Processing helix chain 'E' and resid 1116 through 1118 No H-bonds generated for 'chain 'E' and resid 1116 through 1118' Processing helix chain 'E' and resid 1140 through 1145 removed outlier: 4.040A pdb=" N GLU E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.948A pdb=" N LEU B 88 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 132 Processing helix chain 'B' and resid 188 through 194 removed outlier: 3.677A pdb=" N HIS B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.666A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.650A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.521A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.517A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 854 Processing helix chain 'C' and resid 866 through 883 Processing helix chain 'C' and resid 887 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.505A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.587A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1147 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 365 through 371 removed outlier: 4.236A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.531A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 755 Processing helix chain 'D' and resid 758 through 783 Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 849 through 856 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 891 removed outlier: 3.730A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 removed outlier: 3.522A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 941 removed outlier: 3.624A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.625A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 982 Processing helix chain 'D' and resid 985 through 1033 Processing helix chain 'D' and resid 1116 through 1118 No H-bonds generated for 'chain 'D' and resid 1116 through 1118' Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 4.245A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 27 through 30 removed outlier: 4.252A pdb=" N ALA E 27 " --> pdb=" O TRP E 64 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL E 267 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA E 264 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS E 195 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 48 through 55 removed outlier: 3.601A pdb=" N VAL E 289 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 85 removed outlier: 3.923A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS E 131 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 156 through 157 removed outlier: 3.671A pdb=" N GLU E 156 " --> pdb=" O GLY E 142 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY E 142 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU E 141 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU E 244 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR E 259 " --> pdb=" O HIS E 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.600A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER E 596 " --> pdb=" O LEU E 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 325 through 328 Processing sheet with id=AA7, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.055A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR E 508 " --> pdb=" O ILE E 402 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA E 435 " --> pdb=" O THR E 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.678A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 654 through 660 removed outlier: 4.356A pdb=" N THR E 696 " --> pdb=" O VAL E 656 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN E 658 " --> pdb=" O THR E 696 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'E' and resid 711 through 728 removed outlier: 3.661A pdb=" N ILE E 714 " --> pdb=" O LYS E1073 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS E1073 " --> pdb=" O ILE E 714 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR E 724 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU E1063 " --> pdb=" O THR E 724 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE E 726 " --> pdb=" O VAL E1061 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL E1061 " --> pdb=" O ILE E 726 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY E1059 " --> pdb=" O PRO E 728 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 711 through 728 removed outlier: 3.661A pdb=" N ILE E 714 " --> pdb=" O LYS E1073 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS E1073 " --> pdb=" O ILE E 714 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR E 724 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU E1063 " --> pdb=" O THR E 724 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE E 726 " --> pdb=" O VAL E1061 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL E1061 " --> pdb=" O ILE E 726 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY E1059 " --> pdb=" O PRO E 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'E' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'E' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.653A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 5 " --> pdb=" O LYS A 23 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.830A pdb=" N MET A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TRP A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TRP A 36 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 59 " --> pdb=" O TRP A 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.752A pdb=" N GLY A 98 " --> pdb=" O TYR A 108 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 108 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 126 through 130 removed outlier: 3.523A pdb=" N LYS A 149 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 145 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY A 150 " --> pdb=" O TYR A 181 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TYR A 181 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 126 through 130 removed outlier: 3.523A pdb=" N LYS A 149 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 145 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY A 150 " --> pdb=" O TYR A 181 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TYR A 181 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 157 through 160 removed outlier: 4.801A pdb=" N VAL A 199 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 214 " --> pdb=" O CYS A 201 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.596A pdb=" N SER B 22 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 19 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.584A pdb=" N GLU B 110 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY B 89 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP B 40 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 119 through 123 removed outlier: 6.390A pdb=" N TYR B 178 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER B 181 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 167 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 158 through 159 removed outlier: 6.317A pdb=" N HIS B 203 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N SER B 208 " --> pdb=" O HIS B 203 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.986A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.690A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.666A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.666A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.573A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.980A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.399A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.612A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.912A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 701 through 704 removed outlier: 3.545A pdb=" N LYS D 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.853A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE7, first strand: chain 'D' and resid 28 through 31 removed outlier: 4.059A pdb=" N SER D 60 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.673A pdb=" N VAL D 289 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 83 through 85 removed outlier: 3.884A pdb=" N LEU D 141 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 244 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 246 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 83 through 85 removed outlier: 5.906A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 311 through 317 removed outlier: 3.534A pdb=" N GLY D 311 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR D 599 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR D 315 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 325 through 328 removed outlier: 4.980A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.864A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN D 394 " --> pdb=" O GLU D 516 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE D 402 " --> pdb=" O TYR D 508 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.834A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AF7, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AF8, first strand: chain 'D' and resid 654 through 655 removed outlier: 5.989A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 711 through 728 removed outlier: 3.606A pdb=" N ILE D 714 " --> pdb=" O LYS D1073 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS D1073 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN D1071 " --> pdb=" O THR D 716 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE D 718 " --> pdb=" O PRO D1069 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE D 720 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR D1067 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL D 722 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL D1065 " --> pdb=" O VAL D 722 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR D 724 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU D1063 " --> pdb=" O THR D 724 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE D 726 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL D1061 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY D1059 " --> pdb=" O PRO D 728 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 711 through 728 removed outlier: 3.606A pdb=" N ILE D 714 " --> pdb=" O LYS D1073 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS D1073 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN D1071 " --> pdb=" O THR D 716 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE D 718 " --> pdb=" O PRO D1069 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE D 720 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR D1067 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL D 722 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL D1065 " --> pdb=" O VAL D 722 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR D 724 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU D1063 " --> pdb=" O THR D 724 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE D 726 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL D1061 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY D1059 " --> pdb=" O PRO D 728 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.025A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 1120 through 1122 1109 hydrogen bonds defined for protein. 3072 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: 16.08 Time building geometry restraints manager: 12.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9208 1.34 - 1.46: 7103 1.46 - 1.58: 12625 1.58 - 1.70: 0 1.70 - 1.82: 165 Bond restraints: 29101 Sorted by residual: bond pdb=" C1 NAG E1301 " pdb=" O5 NAG E1301 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" N ASP B 1 " pdb=" CA ASP B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N GLN E 14 " pdb=" CA GLN E 14 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N GLN D 14 " pdb=" CA GLN D 14 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N GLU A 1 " pdb=" CA GLU A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 ... (remaining 29096 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.15: 862 107.15 - 113.86: 16075 113.86 - 120.58: 10953 120.58 - 127.30: 11422 127.30 - 134.01: 294 Bond angle restraints: 39606 Sorted by residual: angle pdb=" C ARG C 21 " pdb=" CA ARG C 21 " pdb=" CB ARG C 21 " ideal model delta sigma weight residual 115.79 111.09 4.70 1.19e+00 7.06e-01 1.56e+01 angle pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" C VAL C 213 " ideal model delta sigma weight residual 111.56 108.31 3.25 8.60e-01 1.35e+00 1.43e+01 angle pdb=" N ILE C 666 " pdb=" CA ILE C 666 " pdb=" C ILE C 666 " ideal model delta sigma weight residual 111.62 108.82 2.80 7.90e-01 1.60e+00 1.25e+01 angle pdb=" N ILE E 666 " pdb=" CA ILE E 666 " pdb=" C ILE E 666 " ideal model delta sigma weight residual 111.56 108.59 2.97 8.60e-01 1.35e+00 1.19e+01 angle pdb=" N VAL D 341 " pdb=" CA VAL D 341 " pdb=" C VAL D 341 " ideal model delta sigma weight residual 111.62 109.02 2.60 7.90e-01 1.60e+00 1.09e+01 ... (remaining 39601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 16857 16.94 - 33.87: 391 33.87 - 50.81: 93 50.81 - 67.75: 25 67.75 - 84.68: 8 Dihedral angle restraints: 17374 sinusoidal: 6773 harmonic: 10601 Sorted by residual: dihedral pdb=" CA ASN E 148 " pdb=" C ASN E 148 " pdb=" N ASN E 149 " pdb=" CA ASN E 149 " ideal model delta harmonic sigma weight residual 180.00 152.44 27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CB CYS A 146 " pdb=" SG CYS A 146 " pdb=" SG CYS A 201 " pdb=" CB CYS A 201 " ideal model delta sinusoidal sigma weight residual 93.00 53.93 39.07 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 61.12 31.88 1 1.00e+01 1.00e-02 1.45e+01 ... (remaining 17371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2835 0.029 - 0.057: 1110 0.057 - 0.086: 138 0.086 - 0.115: 302 0.115 - 0.143: 97 Chirality restraints: 4482 Sorted by residual: chirality pdb=" CA ILE E 714 " pdb=" N ILE E 714 " pdb=" C ILE E 714 " pdb=" CB ILE E 714 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE D 714 " pdb=" N ILE D 714 " pdb=" C ILE D 714 " pdb=" CB ILE D 714 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE C 664 " pdb=" N ILE C 664 " pdb=" C ILE C 664 " pdb=" CB ILE C 664 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 4479 not shown) Planarity restraints: 5139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 916 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C LEU E 916 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU E 916 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR E 917 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 986 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO E 987 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 987 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 987 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 61 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 62 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 62 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 62 " 0.017 5.00e-02 4.00e+02 ... (remaining 5136 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 195 2.57 - 3.16: 23448 3.16 - 3.74: 42621 3.74 - 4.32: 60796 4.32 - 4.90: 102793 Nonbonded interactions: 229853 Sorted by model distance: nonbonded pdb=" OH TYR D 756 " pdb=" OD1 ASP D 994 " model vdw 1.993 3.040 nonbonded pdb=" OH TYR E 756 " pdb=" OD1 ASP E 994 " model vdw 1.999 3.040 nonbonded pdb=" OG SER C 383 " pdb=" OD1 ASP D 985 " model vdw 2.012 3.040 nonbonded pdb=" OD1 ASP E 985 " pdb=" OG SER D 383 " model vdw 2.014 3.040 nonbonded pdb=" OG SER E 813 " pdb=" OE1 GLU E 868 " model vdw 2.024 3.040 ... (remaining 229848 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: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 16 through 827 or resid 849 through 1147)) selection = (chain 'E' and (resid 16 through 247 or resid 255 through 827 or resid 849 throu \ gh 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.400 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: 0.040 Extract box with map and model: 1.200 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 85.410 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.130 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4879 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 : 0.002 0.037 29101 Z= 0.123 Angle : 0.436 5.490 39606 Z= 0.252 Chirality : 0.041 0.143 4482 Planarity : 0.002 0.033 5138 Dihedral : 8.283 84.683 10430 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.25 % Favored : 97.56 % Rotamer: Outliers : 0.03 % Allowed : 0.00 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.14), residues: 3605 helix: 2.57 (0.21), residues: 650 sheet: 0.89 (0.17), residues: 892 loop : -0.02 (0.14), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 47 HIS 0.003 0.000 HIS B 31 PHE 0.009 0.001 PHE D 490 TYR 0.009 0.001 TYR E 144 ARG 0.004 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 844 time to evaluate : 3.159 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 105 ILE cc_start: 0.8784 (mt) cc_final: 0.8496 (tt) REVERT: E 117 LEU cc_start: 0.8542 (tp) cc_final: 0.8291 (tt) REVERT: E 196 ASN cc_start: 0.6015 (t0) cc_final: 0.5792 (m-40) REVERT: E 287 ASP cc_start: 0.8227 (t0) cc_final: 0.8008 (m-30) REVERT: E 493 GLN cc_start: 0.8638 (mt0) cc_final: 0.8400 (mp10) REVERT: E 532 ASN cc_start: 0.7972 (m-40) cc_final: 0.7746 (p0) REVERT: E 666 ILE cc_start: 0.4044 (mt) cc_final: 0.3805 (mt) REVERT: E 720 ILE cc_start: 0.8395 (mm) cc_final: 0.7962 (pt) REVERT: E 736 VAL cc_start: 0.3567 (t) cc_final: 0.3099 (p) REVERT: E 804 GLN cc_start: 0.7379 (mm-40) cc_final: 0.6850 (mm-40) REVERT: E 858 LEU cc_start: -0.0318 (mp) cc_final: -0.0872 (mt) REVERT: E 898 PHE cc_start: 0.7645 (t80) cc_final: 0.7407 (t80) REVERT: E 963 VAL cc_start: 0.5475 (t) cc_final: 0.5079 (t) REVERT: E 1017 GLU cc_start: 0.6669 (mm-30) cc_final: 0.2748 (pt0) REVERT: E 1028 LYS cc_start: 0.6656 (mttt) cc_final: 0.6288 (mtpt) REVERT: E 1029 MET cc_start: 0.8002 (tpp) cc_final: 0.7785 (mmp) REVERT: E 1038 LYS cc_start: 0.8756 (mttm) cc_final: 0.8476 (mmtm) REVERT: E 1062 PHE cc_start: 0.7423 (m-10) cc_final: 0.7144 (m-10) REVERT: A 177 GLN cc_start: 0.0825 (tp40) cc_final: 0.0529 (tt0) REVERT: A 195 PRO cc_start: 0.4340 (Cg_endo) cc_final: 0.4049 (Cg_exo) REVERT: B 47 GLN cc_start: 0.5868 (mt0) cc_final: 0.5658 (tp40) REVERT: B 58 ASN cc_start: 0.3626 (m-40) cc_final: 0.3128 (m-40) REVERT: B 108 LYS cc_start: 0.5902 (tttt) cc_final: 0.5525 (tptp) REVERT: B 111 ILE cc_start: 0.4729 (mm) cc_final: 0.4054 (mt) REVERT: B 162 ASN cc_start: 0.6184 (m-40) cc_final: 0.5886 (t0) REVERT: C 169 GLU cc_start: 0.8548 (tt0) cc_final: 0.8340 (tm-30) REVERT: C 193 VAL cc_start: 0.7605 (t) cc_final: 0.7387 (t) REVERT: C 238 PHE cc_start: 0.7762 (p90) cc_final: 0.7530 (p90) REVERT: C 302 THR cc_start: 0.6181 (m) cc_final: 0.5973 (p) REVERT: C 303 LEU cc_start: 0.6058 (mt) cc_final: 0.5843 (mm) REVERT: C 382 VAL cc_start: 0.5283 (m) cc_final: 0.4961 (p) REVERT: C 546 LEU cc_start: 0.6468 (tp) cc_final: 0.6218 (tt) REVERT: C 559 PHE cc_start: -0.1872 (m-10) cc_final: -0.2258 (m-10) REVERT: C 597 VAL cc_start: 0.5596 (t) cc_final: 0.5328 (t) REVERT: C 599 THR cc_start: 0.2900 (t) cc_final: 0.1734 (t) REVERT: C 654 GLU cc_start: 0.7913 (tt0) cc_final: 0.7697 (mm-30) REVERT: C 664 ILE cc_start: 0.2927 (mt) cc_final: 0.2669 (mt) REVERT: C 752 LEU cc_start: 0.8243 (mt) cc_final: 0.7953 (tp) REVERT: C 772 VAL cc_start: 0.8841 (t) cc_final: 0.8364 (t) REVERT: C 773 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8793 (mm-30) REVERT: C 859 THR cc_start: 0.6646 (m) cc_final: 0.6248 (p) REVERT: C 867 ASP cc_start: 0.7626 (m-30) cc_final: 0.7383 (p0) REVERT: C 947 LYS cc_start: 0.9039 (mttt) cc_final: 0.8468 (mtpt) REVERT: C 957 GLN cc_start: 0.9344 (mt0) cc_final: 0.9067 (pt0) REVERT: C 984 LEU cc_start: 0.5759 (mp) cc_final: 0.5540 (mt) REVERT: C 997 ILE cc_start: 0.7275 (mt) cc_final: 0.6344 (mm) REVERT: C 1002 GLN cc_start: 0.8758 (mp10) cc_final: 0.8541 (pt0) REVERT: C 1013 ILE cc_start: 0.9025 (mt) cc_final: 0.8598 (mt) REVERT: D 225 PRO cc_start: 0.4503 (Cg_exo) cc_final: 0.4240 (Cg_endo) REVERT: D 302 THR cc_start: 0.6535 (m) cc_final: 0.5813 (p) REVERT: D 532 ASN cc_start: 0.7564 (m-40) cc_final: 0.7254 (t0) REVERT: D 572 THR cc_start: 0.6788 (p) cc_final: 0.6451 (m) REVERT: D 710 ASN cc_start: 0.7253 (m110) cc_final: 0.7028 (t0) REVERT: D 723 THR cc_start: 0.8642 (m) cc_final: 0.8420 (p) REVERT: D 736 VAL cc_start: 0.6594 (t) cc_final: 0.6353 (t) REVERT: D 737 ASP cc_start: 0.8401 (t0) cc_final: 0.7985 (p0) REVERT: D 753 LEU cc_start: 0.2329 (tp) cc_final: 0.1753 (tp) REVERT: D 756 TYR cc_start: 0.2430 (m-80) cc_final: 0.1608 (m-10) REVERT: D 759 PHE cc_start: 0.5781 (m-10) cc_final: 0.4689 (m-80) REVERT: D 777 ASN cc_start: 0.8838 (m-40) cc_final: 0.8451 (m-40) REVERT: D 787 GLN cc_start: 0.7973 (mt0) cc_final: 0.7531 (mt0) REVERT: D 874 THR cc_start: 0.9261 (m) cc_final: 0.9058 (p) REVERT: D 947 LYS cc_start: 0.9164 (mttt) cc_final: 0.8944 (mmtm) REVERT: D 980 ILE cc_start: 0.4793 (mt) cc_final: 0.2753 (mt) REVERT: D 984 LEU cc_start: 0.4822 (mt) cc_final: 0.3653 (mp) REVERT: D 1010 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7979 (tp-100) REVERT: D 1036 GLN cc_start: 0.6641 (tt0) cc_final: 0.6149 (tt0) REVERT: D 1061 VAL cc_start: 0.8639 (t) cc_final: 0.8268 (t) REVERT: D 1065 VAL cc_start: 0.9217 (t) cc_final: 0.8466 (t) REVERT: D 1073 LYS cc_start: 0.8569 (tttt) cc_final: 0.8049 (tptt) outliers start: 1 outliers final: 0 residues processed: 845 average time/residue: 0.4365 time to fit residues: 564.1621 Evaluate side-chains 417 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 8.9990 chunk 273 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 282 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 327 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS E 394 ASN E 710 ASN ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1083 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 194 HIS C 188 ASN C 207 HIS C 394 ASN C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 606 ASN C 784 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 928 ASN C1010 GLN C1088 HIS C1101 HIS C1142 GLN D 52 GLN D 66 HIS D 69 HIS D 245 HIS D 856 ASN ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 ASN D1023 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5098 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 29101 Z= 0.443 Angle : 0.845 12.725 39606 Z= 0.444 Chirality : 0.051 0.269 4482 Planarity : 0.006 0.086 5138 Dihedral : 5.063 58.854 3925 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.13 % Favored : 95.67 % Rotamer: Outliers : 0.19 % Allowed : 3.11 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.13), residues: 3605 helix: 0.91 (0.19), residues: 711 sheet: 0.44 (0.16), residues: 902 loop : -0.48 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 50 HIS 0.008 0.003 HIS A 170 PHE 0.027 0.003 PHE C1052 TYR 0.038 0.003 TYR E 145 ARG 0.018 0.002 ARG C1014 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 435 time to evaluate : 3.190 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: E 105 ILE cc_start: 0.9106 (mt) cc_final: 0.8903 (tp) REVERT: E 493 GLN cc_start: 0.8606 (mt0) cc_final: 0.8259 (mp10) REVERT: E 763 LEU cc_start: 0.7949 (mt) cc_final: 0.7556 (mt) REVERT: E 864 LEU cc_start: 0.5969 (tp) cc_final: 0.5733 (tp) REVERT: E 878 LEU cc_start: 0.7017 (tp) cc_final: 0.6578 (tp) REVERT: E 919 ASN cc_start: 0.9262 (m-40) cc_final: 0.9041 (t0) REVERT: E 949 GLN cc_start: 0.8419 (tp40) cc_final: 0.8071 (mm-40) REVERT: E 1013 ILE cc_start: 0.7482 (mt) cc_final: 0.7198 (mt) REVERT: E 1028 LYS cc_start: 0.6396 (mttt) cc_final: 0.6149 (mttm) REVERT: E 1029 MET cc_start: 0.7955 (tpp) cc_final: 0.7726 (mmm) REVERT: E 1033 VAL cc_start: 0.3548 (t) cc_final: 0.2461 (t) REVERT: E 1038 LYS cc_start: 0.8924 (mttm) cc_final: 0.8569 (mmtm) REVERT: E 1047 TYR cc_start: 0.7909 (m-80) cc_final: 0.7706 (m-10) REVERT: E 1062 PHE cc_start: 0.7026 (m-10) cc_final: 0.6822 (m-80) REVERT: A 73 ASP cc_start: 0.7322 (p0) cc_final: 0.7036 (p0) REVERT: B 58 ASN cc_start: 0.3998 (m-40) cc_final: 0.3598 (m-40) REVERT: B 162 ASN cc_start: 0.6520 (m-40) cc_final: 0.6155 (t0) REVERT: C 238 PHE cc_start: 0.7682 (p90) cc_final: 0.7401 (p90) REVERT: C 302 THR cc_start: 0.6451 (m) cc_final: 0.6163 (p) REVERT: C 731 MET cc_start: 0.8064 (ttm) cc_final: 0.7861 (ttm) REVERT: C 822 LEU cc_start: 0.8000 (mt) cc_final: 0.7695 (mt) REVERT: C 997 ILE cc_start: 0.7546 (mt) cc_final: 0.7130 (mt) REVERT: C 1006 THR cc_start: 0.9204 (p) cc_final: 0.8848 (p) REVERT: C 1013 ILE cc_start: 0.9070 (mt) cc_final: 0.8544 (mt) REVERT: C 1017 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8872 (pm20) REVERT: C 1018 ILE cc_start: 0.8868 (mt) cc_final: 0.8543 (tt) REVERT: C 1031 GLU cc_start: 0.8502 (mt-10) cc_final: 0.7902 (mt-10) REVERT: C 1042 PHE cc_start: 0.7151 (t80) cc_final: 0.6587 (t80) REVERT: C 1052 PHE cc_start: 0.8254 (m-10) cc_final: 0.7987 (m-10) REVERT: D 98 SER cc_start: 0.7241 (m) cc_final: 0.6529 (t) REVERT: D 177 MET cc_start: 0.2594 (mpp) cc_final: 0.2050 (mtm) REVERT: D 464 PHE cc_start: 0.8478 (m-80) cc_final: 0.8096 (m-10) REVERT: D 697 MET cc_start: 0.2634 (ttm) cc_final: 0.2357 (mtp) REVERT: D 723 THR cc_start: 0.8729 (m) cc_final: 0.8408 (p) REVERT: D 731 MET cc_start: 0.6716 (ttp) cc_final: 0.5063 (ttm) REVERT: D 737 ASP cc_start: 0.8642 (t0) cc_final: 0.8360 (p0) REVERT: D 817 PHE cc_start: 0.7547 (t80) cc_final: 0.7317 (t80) REVERT: D 875 SER cc_start: 0.8959 (t) cc_final: 0.8621 (p) REVERT: D 904 TYR cc_start: 0.8069 (t80) cc_final: 0.7576 (t80) REVERT: D 947 LYS cc_start: 0.9270 (mttt) cc_final: 0.8905 (mmtm) REVERT: D 1001 LEU cc_start: 0.7734 (mt) cc_final: 0.7370 (mt) REVERT: D 1029 MET cc_start: 0.8589 (tmm) cc_final: 0.8197 (tmm) outliers start: 6 outliers final: 1 residues processed: 441 average time/residue: 0.4169 time to fit residues: 287.9553 Evaluate side-chains 250 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 248 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 272 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 328 optimal weight: 1.9990 chunk 354 optimal weight: 0.9990 chunk 292 optimal weight: 7.9990 chunk 325 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 263 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1002 GLN ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN B 47 GLN B 95 GLN C 394 ASN C 481 ASN C1002 GLN C1010 GLN C1101 HIS D 450 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 856 ASN ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5053 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29101 Z= 0.203 Angle : 0.570 10.886 39606 Z= 0.298 Chirality : 0.044 0.166 4482 Planarity : 0.004 0.069 5138 Dihedral : 4.506 57.237 3925 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.19 % Favored : 96.62 % Rotamer: Outliers : 0.03 % Allowed : 1.85 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.13), residues: 3605 helix: 1.14 (0.19), residues: 717 sheet: 0.39 (0.16), residues: 933 loop : -0.48 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 50 HIS 0.006 0.001 HIS C1101 PHE 0.040 0.002 PHE E 342 TYR 0.024 0.002 TYR E 873 ARG 0.007 0.001 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 384 time to evaluate : 3.193 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: E 105 ILE cc_start: 0.8998 (mt) cc_final: 0.8782 (tp) REVERT: E 340 GLU cc_start: 0.8074 (pt0) cc_final: 0.7694 (pp20) REVERT: E 490 PHE cc_start: 0.2485 (t80) cc_final: 0.2242 (t80) REVERT: E 493 GLN cc_start: 0.8682 (mt0) cc_final: 0.8408 (mp10) REVERT: E 718 PHE cc_start: 0.9021 (p90) cc_final: 0.8753 (p90) REVERT: E 725 GLU cc_start: 0.7032 (tt0) cc_final: 0.6795 (tt0) REVERT: E 878 LEU cc_start: 0.7882 (tp) cc_final: 0.7664 (tp) REVERT: E 949 GLN cc_start: 0.8404 (tp40) cc_final: 0.8075 (mm110) REVERT: E 1017 GLU cc_start: 0.6710 (mm-30) cc_final: 0.5152 (tt0) REVERT: E 1018 ILE cc_start: 0.2945 (mm) cc_final: 0.2473 (mm) REVERT: E 1028 LYS cc_start: 0.6150 (mttt) cc_final: 0.5947 (mttm) REVERT: E 1033 VAL cc_start: 0.4009 (t) cc_final: 0.3437 (t) REVERT: E 1038 LYS cc_start: 0.8860 (mttm) cc_final: 0.8548 (mmtm) REVERT: A 73 ASP cc_start: 0.7365 (p0) cc_final: 0.7074 (p0) REVERT: B 58 ASN cc_start: 0.4235 (m-40) cc_final: 0.3777 (m-40) REVERT: B 162 ASN cc_start: 0.6555 (m-40) cc_final: 0.6194 (t0) REVERT: C 238 PHE cc_start: 0.7662 (p90) cc_final: 0.7140 (p90) REVERT: C 269 TYR cc_start: 0.7628 (m-80) cc_final: 0.6983 (m-80) REVERT: C 613 GLN cc_start: 0.7261 (mp-120) cc_final: 0.7017 (mp10) REVERT: C 725 GLU cc_start: 0.8109 (tp30) cc_final: 0.7850 (tp30) REVERT: C 752 LEU cc_start: 0.8350 (mt) cc_final: 0.7898 (tp) REVERT: C 957 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8301 (tp-100) REVERT: C 997 ILE cc_start: 0.7272 (mt) cc_final: 0.6895 (mt) REVERT: C 1018 ILE cc_start: 0.8614 (mt) cc_final: 0.8265 (tt) REVERT: C 1055 SER cc_start: 0.6252 (t) cc_final: 0.6024 (t) REVERT: D 464 PHE cc_start: 0.8435 (m-80) cc_final: 0.8117 (m-10) REVERT: D 723 THR cc_start: 0.8600 (m) cc_final: 0.8329 (p) REVERT: D 735 SER cc_start: 0.7296 (m) cc_final: 0.6937 (m) REVERT: D 737 ASP cc_start: 0.8591 (t0) cc_final: 0.8307 (p0) REVERT: D 909 ILE cc_start: 0.8922 (pt) cc_final: 0.8414 (mt) REVERT: D 947 LYS cc_start: 0.9318 (mttt) cc_final: 0.8924 (mmtm) REVERT: D 1089 PHE cc_start: 0.8897 (m-80) cc_final: 0.8306 (m-80) outliers start: 1 outliers final: 0 residues processed: 385 average time/residue: 0.4135 time to fit residues: 255.7108 Evaluate side-chains 252 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 9.9990 chunk 246 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 329 optimal weight: 4.9990 chunk 348 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 312 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 955 ASN ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN C 394 ASN C 542 ASN C1002 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 856 ASN ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5071 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 29101 Z= 0.220 Angle : 0.566 12.156 39606 Z= 0.295 Chirality : 0.044 0.195 4482 Planarity : 0.004 0.063 5138 Dihedral : 4.526 56.982 3925 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.86 % Favored : 95.98 % Rotamer: Outliers : 0.06 % Allowed : 1.95 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.13), residues: 3605 helix: 1.06 (0.20), residues: 722 sheet: 0.39 (0.16), residues: 905 loop : -0.58 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 64 HIS 0.007 0.001 HIS E1048 PHE 0.024 0.002 PHE D 855 TYR 0.022 0.002 TYR E 873 ARG 0.008 0.001 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 345 time to evaluate : 3.398 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 105 ILE cc_start: 0.9030 (mt) cc_final: 0.8797 (tp) REVERT: E 493 GLN cc_start: 0.8704 (mt0) cc_final: 0.8393 (mp-120) REVERT: E 725 GLU cc_start: 0.6762 (tt0) cc_final: 0.6518 (tt0) REVERT: E 731 MET cc_start: -0.1163 (tmm) cc_final: -0.1670 (tmm) REVERT: E 864 LEU cc_start: 0.6559 (tp) cc_final: 0.6324 (tt) REVERT: E 1018 ILE cc_start: 0.3176 (mm) cc_final: 0.2829 (mm) REVERT: E 1038 LYS cc_start: 0.8894 (mttm) cc_final: 0.8533 (mmtm) REVERT: A 73 ASP cc_start: 0.7423 (p0) cc_final: 0.7173 (p0) REVERT: A 78 THR cc_start: 0.5922 (m) cc_final: 0.5686 (m) REVERT: B 58 ASN cc_start: 0.4283 (m-40) cc_final: 0.3885 (m-40) REVERT: B 149 ILE cc_start: 0.2296 (tt) cc_final: 0.2031 (tt) REVERT: B 162 ASN cc_start: 0.6609 (m-40) cc_final: 0.6214 (t0) REVERT: C 238 PHE cc_start: 0.7282 (p90) cc_final: 0.6805 (p90) REVERT: C 269 TYR cc_start: 0.7420 (m-80) cc_final: 0.7212 (m-80) REVERT: C 725 GLU cc_start: 0.8151 (tp30) cc_final: 0.7877 (tp30) REVERT: C 752 LEU cc_start: 0.8266 (mt) cc_final: 0.7858 (tp) REVERT: C 904 TYR cc_start: 0.8313 (t80) cc_final: 0.8089 (t80) REVERT: C 957 GLN cc_start: 0.8760 (tp-100) cc_final: 0.8351 (tp-100) REVERT: C 997 ILE cc_start: 0.7249 (mt) cc_final: 0.6907 (mt) REVERT: C 1018 ILE cc_start: 0.8632 (mt) cc_final: 0.8272 (tt) REVERT: C 1031 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7950 (mt-10) REVERT: D 177 MET cc_start: 0.2721 (mpp) cc_final: 0.2460 (mtm) REVERT: D 464 PHE cc_start: 0.8429 (m-80) cc_final: 0.8102 (m-10) REVERT: D 723 THR cc_start: 0.8647 (m) cc_final: 0.8370 (p) REVERT: D 737 ASP cc_start: 0.8635 (t0) cc_final: 0.8378 (p0) REVERT: D 909 ILE cc_start: 0.8861 (pt) cc_final: 0.8417 (mt) REVERT: D 947 LYS cc_start: 0.9386 (mttt) cc_final: 0.8919 (mmtm) REVERT: D 1006 THR cc_start: 0.8774 (m) cc_final: 0.8564 (p) REVERT: D 1089 PHE cc_start: 0.8956 (m-80) cc_final: 0.8405 (m-80) outliers start: 2 outliers final: 1 residues processed: 346 average time/residue: 0.3952 time to fit residues: 222.8668 Evaluate side-chains 226 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 3.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 259 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 297 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 313 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 895 GLN ** E 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 895 GLN ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5081 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29101 Z= 0.209 Angle : 0.556 13.011 39606 Z= 0.290 Chirality : 0.044 0.184 4482 Planarity : 0.004 0.050 5138 Dihedral : 4.529 58.100 3925 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.91 % Favored : 95.89 % Rotamer: Outliers : 0.03 % Allowed : 1.48 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.13), residues: 3605 helix: 1.05 (0.20), residues: 719 sheet: 0.33 (0.16), residues: 895 loop : -0.64 (0.13), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 50 HIS 0.008 0.001 HIS C1101 PHE 0.020 0.002 PHE E 329 TYR 0.039 0.002 TYR E1047 ARG 0.008 0.001 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 3.322 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: E 105 ILE cc_start: 0.9022 (mt) cc_final: 0.8783 (tp) REVERT: E 493 GLN cc_start: 0.8662 (mt0) cc_final: 0.8419 (mp10) REVERT: E 697 MET cc_start: 0.8322 (tpt) cc_final: 0.7996 (tpt) REVERT: E 763 LEU cc_start: 0.7730 (mt) cc_final: 0.7492 (mt) REVERT: E 949 GLN cc_start: 0.8472 (tp40) cc_final: 0.8183 (mm110) REVERT: E 1038 LYS cc_start: 0.8939 (mttm) cc_final: 0.8570 (mmtm) REVERT: A 73 ASP cc_start: 0.7445 (p0) cc_final: 0.7215 (p0) REVERT: B 58 ASN cc_start: 0.4416 (m-40) cc_final: 0.4084 (m-40) REVERT: B 162 ASN cc_start: 0.6825 (m-40) cc_final: 0.6375 (t0) REVERT: C 238 PHE cc_start: 0.7281 (p90) cc_final: 0.6824 (p90) REVERT: C 269 TYR cc_start: 0.7383 (m-80) cc_final: 0.7147 (m-80) REVERT: C 725 GLU cc_start: 0.8111 (tp30) cc_final: 0.7763 (tp30) REVERT: C 752 LEU cc_start: 0.8003 (mt) cc_final: 0.7629 (tp) REVERT: C 957 GLN cc_start: 0.8752 (tp-100) cc_final: 0.8328 (tp-100) REVERT: C 984 LEU cc_start: 0.6191 (tp) cc_final: 0.5986 (tp) REVERT: C 1018 ILE cc_start: 0.8645 (mt) cc_final: 0.8264 (tt) REVERT: C 1031 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7966 (mt-10) REVERT: D 177 MET cc_start: 0.2663 (mpp) cc_final: 0.2373 (mtm) REVERT: D 464 PHE cc_start: 0.8420 (m-80) cc_final: 0.8123 (m-10) REVERT: D 723 THR cc_start: 0.8600 (m) cc_final: 0.8353 (p) REVERT: D 737 ASP cc_start: 0.8643 (t0) cc_final: 0.8416 (p0) REVERT: D 909 ILE cc_start: 0.8827 (pt) cc_final: 0.8418 (mt) REVERT: D 947 LYS cc_start: 0.9399 (mttt) cc_final: 0.8943 (mmtm) REVERT: D 1089 PHE cc_start: 0.8944 (m-80) cc_final: 0.8454 (m-80) outliers start: 1 outliers final: 1 residues processed: 331 average time/residue: 0.3753 time to fit residues: 203.4412 Evaluate side-chains 228 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 3.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 6.9990 chunk 314 optimal weight: 0.0870 chunk 68 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 349 optimal weight: 4.9990 chunk 289 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 GLN E 245 HIS E 394 ASN ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 895 GLN C1002 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5104 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29101 Z= 0.243 Angle : 0.585 12.979 39606 Z= 0.307 Chirality : 0.044 0.251 4482 Planarity : 0.004 0.049 5138 Dihedral : 4.681 57.391 3925 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.36 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 3605 helix: 0.90 (0.19), residues: 728 sheet: 0.20 (0.16), residues: 894 loop : -0.71 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 50 HIS 0.009 0.001 HIS C1101 PHE 0.047 0.002 PHE E1062 TYR 0.020 0.002 TYR E1047 ARG 0.007 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 3.395 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: E 105 ILE cc_start: 0.9019 (mt) cc_final: 0.8770 (tp) REVERT: E 493 GLN cc_start: 0.8629 (mt0) cc_final: 0.8371 (mp10) REVERT: E 725 GLU cc_start: 0.7110 (tt0) cc_final: 0.6884 (tt0) REVERT: E 752 LEU cc_start: 0.5674 (mt) cc_final: 0.4994 (mt) REVERT: E 949 GLN cc_start: 0.8479 (tp40) cc_final: 0.8249 (mm-40) REVERT: E 1038 LYS cc_start: 0.8988 (mttm) cc_final: 0.8583 (mmtm) REVERT: A 73 ASP cc_start: 0.7511 (p0) cc_final: 0.7302 (p0) REVERT: B 58 ASN cc_start: 0.4801 (m-40) cc_final: 0.4521 (m-40) REVERT: B 162 ASN cc_start: 0.6789 (m-40) cc_final: 0.6372 (t0) REVERT: C 238 PHE cc_start: 0.7413 (p90) cc_final: 0.7024 (p90) REVERT: C 269 TYR cc_start: 0.7403 (m-80) cc_final: 0.7097 (m-80) REVERT: C 725 GLU cc_start: 0.8115 (tp30) cc_final: 0.7775 (tp30) REVERT: C 731 MET cc_start: 0.8121 (ttm) cc_final: 0.7906 (ttm) REVERT: C 752 LEU cc_start: 0.7991 (mt) cc_final: 0.7603 (tp) REVERT: C 957 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8344 (tp-100) REVERT: C 1031 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7948 (mt-10) REVERT: D 177 MET cc_start: 0.2694 (mpp) cc_final: 0.2466 (mtm) REVERT: D 464 PHE cc_start: 0.8442 (m-80) cc_final: 0.8170 (m-10) REVERT: D 723 THR cc_start: 0.8582 (m) cc_final: 0.8353 (p) REVERT: D 875 SER cc_start: 0.8853 (t) cc_final: 0.8570 (p) REVERT: D 909 ILE cc_start: 0.8836 (pt) cc_final: 0.8478 (mt) REVERT: D 947 LYS cc_start: 0.9411 (mttt) cc_final: 0.8917 (mmtm) REVERT: D 1003 SER cc_start: 0.3480 (p) cc_final: 0.3134 (p) REVERT: D 1089 PHE cc_start: 0.8970 (m-80) cc_final: 0.8520 (m-80) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.3753 time to fit residues: 195.8008 Evaluate side-chains 219 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 7.9990 chunk 39 optimal weight: 0.4980 chunk 199 optimal weight: 7.9990 chunk 255 optimal weight: 9.9990 chunk 197 optimal weight: 0.2980 chunk 294 optimal weight: 0.0870 chunk 195 optimal weight: 8.9990 chunk 347 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 212 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 949 GLN ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C 895 GLN C1002 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5079 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29101 Z= 0.173 Angle : 0.547 12.534 39606 Z= 0.281 Chirality : 0.044 0.198 4482 Planarity : 0.004 0.049 5138 Dihedral : 4.496 54.607 3925 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3605 helix: 0.95 (0.20), residues: 723 sheet: 0.25 (0.17), residues: 893 loop : -0.66 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 50 HIS 0.008 0.001 HIS C1101 PHE 0.028 0.001 PHE D 275 TYR 0.019 0.001 TYR E 248 ARG 0.007 0.000 ARG E1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 3.047 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: E 105 ILE cc_start: 0.9002 (mt) cc_final: 0.8752 (tp) REVERT: E 448 ASN cc_start: 0.6515 (t0) cc_final: 0.5323 (m110) REVERT: E 493 GLN cc_start: 0.8603 (mt0) cc_final: 0.8350 (mp10) REVERT: E 731 MET cc_start: -0.0679 (tmm) cc_final: -0.0897 (tmm) REVERT: E 759 PHE cc_start: 0.5616 (m-80) cc_final: 0.4634 (m-80) REVERT: E 949 GLN cc_start: 0.8504 (tp-100) cc_final: 0.8259 (mm-40) REVERT: E 1030 SER cc_start: 0.7557 (p) cc_final: 0.7260 (p) REVERT: E 1038 LYS cc_start: 0.8956 (mttm) cc_final: 0.8598 (mmtm) REVERT: E 1042 PHE cc_start: 0.7857 (t80) cc_final: 0.7642 (t80) REVERT: E 1050 MET cc_start: 0.8251 (pmm) cc_final: 0.7921 (pmm) REVERT: A 73 ASP cc_start: 0.7482 (p0) cc_final: 0.7282 (p0) REVERT: A 78 THR cc_start: 0.5847 (m) cc_final: 0.5633 (m) REVERT: C 238 PHE cc_start: 0.7419 (p90) cc_final: 0.7082 (p90) REVERT: C 269 TYR cc_start: 0.7374 (m-80) cc_final: 0.7064 (m-80) REVERT: C 725 GLU cc_start: 0.8102 (tp30) cc_final: 0.7692 (tp30) REVERT: C 752 LEU cc_start: 0.7919 (mt) cc_final: 0.7489 (tp) REVERT: C 773 GLU cc_start: 0.9138 (pt0) cc_final: 0.8501 (tp30) REVERT: C 774 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8498 (mm-40) REVERT: C 777 ASN cc_start: 0.8795 (m110) cc_final: 0.7729 (m110) REVERT: C 954 GLN cc_start: 0.9431 (tp-100) cc_final: 0.8875 (tp40) REVERT: C 957 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8296 (tp-100) REVERT: C 1018 ILE cc_start: 0.8349 (tt) cc_final: 0.8149 (tt) REVERT: C 1031 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7381 (mt-10) REVERT: C 1034 LEU cc_start: 0.8774 (mm) cc_final: 0.8470 (mm) REVERT: D 464 PHE cc_start: 0.8446 (m-80) cc_final: 0.8174 (m-10) REVERT: D 875 SER cc_start: 0.8801 (t) cc_final: 0.8546 (p) REVERT: D 909 ILE cc_start: 0.8839 (pt) cc_final: 0.8395 (mt) REVERT: D 947 LYS cc_start: 0.9429 (mttt) cc_final: 0.8979 (mmtm) REVERT: D 1089 PHE cc_start: 0.8932 (m-80) cc_final: 0.8520 (m-80) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.3685 time to fit residues: 198.5270 Evaluate side-chains 226 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 237 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 273 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 GLN ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 ASN D1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5097 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29101 Z= 0.201 Angle : 0.563 12.580 39606 Z= 0.293 Chirality : 0.044 0.206 4482 Planarity : 0.004 0.113 5138 Dihedral : 4.569 57.309 3925 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.19 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3605 helix: 0.79 (0.20), residues: 734 sheet: 0.22 (0.17), residues: 884 loop : -0.68 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 50 HIS 0.024 0.001 HIS D1048 PHE 0.024 0.002 PHE E1062 TYR 0.026 0.001 TYR C 873 ARG 0.014 0.001 ARG E1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 3.428 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: E 105 ILE cc_start: 0.8982 (mt) cc_final: 0.8749 (tp) REVERT: E 448 ASN cc_start: 0.6678 (t0) cc_final: 0.5426 (m110) REVERT: E 493 GLN cc_start: 0.8629 (mt0) cc_final: 0.8368 (mp10) REVERT: E 731 MET cc_start: -0.0629 (tmm) cc_final: -0.1119 (tmm) REVERT: E 759 PHE cc_start: 0.5083 (m-80) cc_final: 0.4435 (m-80) REVERT: E 949 GLN cc_start: 0.8500 (tp-100) cc_final: 0.8268 (mm-40) REVERT: E 993 ILE cc_start: 0.9076 (mt) cc_final: 0.8842 (mt) REVERT: E 1038 LYS cc_start: 0.9010 (mttm) cc_final: 0.8617 (mmtm) REVERT: A 177 GLN cc_start: 0.2428 (tp40) cc_final: 0.1339 (pt0) REVERT: C 238 PHE cc_start: 0.7239 (p90) cc_final: 0.7031 (p90) REVERT: C 269 TYR cc_start: 0.7388 (m-80) cc_final: 0.7098 (m-80) REVERT: C 725 GLU cc_start: 0.8100 (tp30) cc_final: 0.7727 (tp30) REVERT: C 731 MET cc_start: 0.8498 (ttm) cc_final: 0.7947 (ttm) REVERT: C 752 LEU cc_start: 0.8044 (mt) cc_final: 0.7655 (tp) REVERT: C 902 MET cc_start: 0.8483 (mmm) cc_final: 0.8100 (mmm) REVERT: C 921 LYS cc_start: 0.9033 (mttt) cc_final: 0.8818 (pttp) REVERT: C 954 GLN cc_start: 0.9446 (tp-100) cc_final: 0.8860 (tp40) REVERT: C 957 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8369 (tp-100) REVERT: D 177 MET cc_start: 0.1991 (mpp) cc_final: 0.1775 (mtm) REVERT: D 464 PHE cc_start: 0.8460 (m-80) cc_final: 0.8188 (m-10) REVERT: D 875 SER cc_start: 0.8881 (t) cc_final: 0.8632 (p) REVERT: D 909 ILE cc_start: 0.8800 (pt) cc_final: 0.8374 (mt) REVERT: D 947 LYS cc_start: 0.9416 (mttt) cc_final: 0.8963 (mmtm) REVERT: D 1089 PHE cc_start: 0.8955 (m-80) cc_final: 0.8493 (m-80) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.3648 time to fit residues: 184.4146 Evaluate side-chains 224 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 0.8980 chunk 333 optimal weight: 5.9990 chunk 304 optimal weight: 2.9990 chunk 324 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 292 optimal weight: 20.0000 chunk 306 optimal weight: 5.9990 chunk 323 optimal weight: 0.0970 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 23 GLN ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 895 GLN C1002 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 ASN ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5121 moved from start: 0.6232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29101 Z= 0.235 Angle : 0.595 12.040 39606 Z= 0.310 Chirality : 0.045 0.189 4482 Planarity : 0.004 0.071 5138 Dihedral : 4.828 58.295 3925 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.69 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3605 helix: 0.76 (0.19), residues: 730 sheet: 0.11 (0.17), residues: 892 loop : -0.77 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 50 HIS 0.022 0.002 HIS D1048 PHE 0.044 0.002 PHE E1062 TYR 0.019 0.002 TYR D 917 ARG 0.014 0.001 ARG E1039 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 3.161 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: E 105 ILE cc_start: 0.8957 (mt) cc_final: 0.8713 (tp) REVERT: E 448 ASN cc_start: 0.6761 (t0) cc_final: 0.5565 (m110) REVERT: E 493 GLN cc_start: 0.8533 (mt0) cc_final: 0.8177 (mp10) REVERT: E 926 GLN cc_start: 0.8340 (mt0) cc_final: 0.8006 (mt0) REVERT: E 949 GLN cc_start: 0.8498 (tp-100) cc_final: 0.8254 (mm-40) REVERT: E 1029 MET cc_start: 0.7555 (mmp) cc_final: 0.6276 (mmp) REVERT: E 1038 LYS cc_start: 0.8928 (mttm) cc_final: 0.8542 (mmtm) REVERT: B 145 TYR cc_start: 0.5112 (t80) cc_final: 0.4611 (t80) REVERT: C 238 PHE cc_start: 0.7350 (p90) cc_final: 0.7101 (p90) REVERT: C 269 TYR cc_start: 0.7380 (m-80) cc_final: 0.7166 (m-80) REVERT: C 725 GLU cc_start: 0.8137 (tp30) cc_final: 0.7785 (tp30) REVERT: C 752 LEU cc_start: 0.7980 (mt) cc_final: 0.7605 (tp) REVERT: C 902 MET cc_start: 0.8515 (mmm) cc_final: 0.8205 (mmm) REVERT: C 921 LYS cc_start: 0.9037 (mttt) cc_final: 0.8833 (pttp) REVERT: C 1051 SER cc_start: 0.7979 (p) cc_final: 0.7699 (t) REVERT: D 177 MET cc_start: 0.1956 (mpp) cc_final: 0.1627 (mtm) REVERT: D 464 PHE cc_start: 0.8483 (m-80) cc_final: 0.8267 (m-10) REVERT: D 765 ARG cc_start: 0.8287 (ptm160) cc_final: 0.7808 (ptm-80) REVERT: D 875 SER cc_start: 0.8924 (t) cc_final: 0.8687 (p) REVERT: D 909 ILE cc_start: 0.8803 (pt) cc_final: 0.8376 (mt) REVERT: D 947 LYS cc_start: 0.9382 (mttt) cc_final: 0.8923 (mmtm) REVERT: D 1089 PHE cc_start: 0.8971 (m-80) cc_final: 0.8497 (m-80) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.3637 time to fit residues: 178.7332 Evaluate side-chains 215 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 8.9990 chunk 342 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 162 optimal weight: 0.2980 chunk 238 optimal weight: 5.9990 chunk 359 optimal weight: 6.9990 chunk 331 optimal weight: 0.4980 chunk 286 optimal weight: 0.0970 chunk 29 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 175 optimal weight: 0.0060 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 23 GLN ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5114 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29101 Z= 0.212 Angle : 0.585 12.101 39606 Z= 0.304 Chirality : 0.044 0.219 4482 Planarity : 0.004 0.067 5138 Dihedral : 4.806 57.768 3925 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.27 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3605 helix: 0.67 (0.19), residues: 735 sheet: 0.07 (0.17), residues: 891 loop : -0.82 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 50 HIS 0.020 0.001 HIS D1048 PHE 0.028 0.002 PHE C1052 TYR 0.023 0.002 TYR C1007 ARG 0.018 0.001 ARG C 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 3.683 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: E 105 ILE cc_start: 0.8952 (mt) cc_final: 0.8699 (tp) REVERT: E 448 ASN cc_start: 0.6750 (t0) cc_final: 0.5603 (m110) REVERT: E 493 GLN cc_start: 0.8543 (mt0) cc_final: 0.8145 (mp10) REVERT: E 926 GLN cc_start: 0.8212 (mt0) cc_final: 0.7980 (mt0) REVERT: E 993 ILE cc_start: 0.9090 (mt) cc_final: 0.8842 (mt) REVERT: E 1038 LYS cc_start: 0.8969 (mttm) cc_final: 0.8583 (mmtm) REVERT: A 177 GLN cc_start: 0.3224 (tp40) cc_final: 0.1967 (pt0) REVERT: B 11 LEU cc_start: 0.4533 (pt) cc_final: 0.4024 (pp) REVERT: B 145 TYR cc_start: 0.5077 (t80) cc_final: 0.4573 (t80) REVERT: C 725 GLU cc_start: 0.8158 (tp30) cc_final: 0.7780 (tp30) REVERT: C 752 LEU cc_start: 0.8095 (mt) cc_final: 0.7712 (tp) REVERT: C 773 GLU cc_start: 0.9267 (pt0) cc_final: 0.8799 (tp30) REVERT: C 774 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8869 (mt0) REVERT: C 902 MET cc_start: 0.8507 (mmm) cc_final: 0.8189 (mmm) REVERT: C 921 LYS cc_start: 0.9025 (mttt) cc_final: 0.8824 (pttp) REVERT: D 177 MET cc_start: 0.2105 (mpp) cc_final: 0.1769 (mtm) REVERT: D 765 ARG cc_start: 0.8392 (ptm160) cc_final: 0.7837 (ptm-80) REVERT: D 875 SER cc_start: 0.8850 (t) cc_final: 0.8623 (p) REVERT: D 909 ILE cc_start: 0.8836 (pt) cc_final: 0.8406 (mt) REVERT: D 947 LYS cc_start: 0.9393 (mttt) cc_final: 0.8941 (mmtm) REVERT: D 1089 PHE cc_start: 0.8969 (m-80) cc_final: 0.8503 (m-80) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.3743 time to fit residues: 181.4275 Evaluate side-chains 210 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 227 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 79 optimal weight: 0.0000 chunk 286 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 294 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 ASN ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 949 GLN ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 HIS A 139 ASN A 170 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.063206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.051187 restraints weight = 246831.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.052319 restraints weight = 161759.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.053143 restraints weight = 115531.490| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29101 Z= 0.207 Angle : 0.576 11.943 39606 Z= 0.299 Chirality : 0.044 0.170 4482 Planarity : 0.004 0.082 5138 Dihedral : 4.818 58.372 3925 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.36 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3605 helix: 0.73 (0.19), residues: 717 sheet: -0.03 (0.17), residues: 896 loop : -0.80 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 50 HIS 0.020 0.001 HIS D1048 PHE 0.038 0.002 PHE E1062 TYR 0.023 0.002 TYR C1007 ARG 0.016 0.001 ARG C1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6271.15 seconds wall clock time: 113 minutes 50.79 seconds (6830.79 seconds total)