Starting phenix.real_space_refine on Fri Feb 23 17:22:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yc5_33734/02_2024/7yc5_33734.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yc5_33734/02_2024/7yc5_33734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yc5_33734/02_2024/7yc5_33734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yc5_33734/02_2024/7yc5_33734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yc5_33734/02_2024/7yc5_33734.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yc5_33734/02_2024/7yc5_33734.pdb" } resolution = 3.1 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= 0.002 sd= 0.202 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 159 5.16 5 C 24808 2.51 5 N 6494 2.21 5 O 7696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39157 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8094 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 56, 'TRANS': 980} Chain breaks: 8 Chain: "B" Number of atoms: 8094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8094 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 56, 'TRANS': 980} Chain breaks: 8 Chain: "C" Number of atoms: 8094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8094 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 56, 'TRANS': 980} Chain breaks: 8 Chain: "D" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3313 Classifications: {'peptide': 441} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 2 Chain: "E" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3313 Classifications: {'peptide': 441} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 2 Chain: "F" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3313 Classifications: {'peptide': 441} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 2 Chain: "G" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1496 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 2 Chain: "H" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1496 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 2 Chain: "I" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1496 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 20.46, per 1000 atoms: 0.52 Number of scatterers: 39157 At special positions: 0 Unit cell: (137.899, 144.208, 248.759, 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 159 16.00 O 7696 8.00 N 6494 7.00 C 24808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.02 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 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 158 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 283 " - pdb=" SG CYS D 350 " distance=2.03 Simple disulfide: pdb=" SG CYS D 398 " - pdb=" SG CYS D 458 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 158 " - pdb=" SG CYS E 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 283 " - pdb=" SG CYS E 350 " distance=2.03 Simple disulfide: pdb=" SG CYS E 398 " - pdb=" SG CYS E 458 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 158 " - pdb=" SG CYS F 225 " distance=2.03 Simple disulfide: pdb=" SG CYS F 283 " - pdb=" SG CYS F 350 " distance=2.03 Simple disulfide: pdb=" SG CYS F 398 " - pdb=" SG CYS F 458 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 154 " - pdb=" SG CYS G 210 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 154 " - pdb=" SG CYS I 210 " 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 A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG B1301 " - " ASN B 343 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG C1401 " - " ASN C 343 " " NAG C1402 " - " ASN C 165 " " NAG C1403 " - " ASN C 282 " " NAG C1404 " - " ASN C 331 " " NAG C1405 " - " ASN C 709 " " NAG C1406 " - " ASN C 801 " " NAG C1407 " - " ASN C1074 " " NAG C1408 " - " ASN C1098 " " NAG C1409 " - " ASN C1134 " Time building additional restraints: 16.65 Conformation dependent library (CDL) restraints added in 7.4 seconds 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9294 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 110 sheets defined 17.7% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.83 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.042A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.658A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.680A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.065A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.200A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.862A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.261A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1148 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.041A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.661A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.775A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 849 through 855 removed outlier: 3.504A pdb=" N GLN B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 887 through 891 removed outlier: 4.151A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.204A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.875A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.273A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1148 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.040A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.660A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 849 through 855 removed outlier: 3.538A pdb=" N GLN C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.226A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.598A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.265A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 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: 3.914A 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 removed outlier: 3.514A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1032 Processing helix chain 'C' and resid 1141 through 1148 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.553A pdb=" N ASP D 90 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 91' Processing helix chain 'D' and resid 216 through 220 removed outlier: 3.525A pdb=" N ASP D 219 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU D 220 " --> pdb=" O SER D 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 216 through 220' Processing helix chain 'D' and resid 385 through 392 removed outlier: 3.617A pdb=" N LEU D 389 " --> pdb=" O SER D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 452 removed outlier: 4.223A pdb=" N GLU D 451 " --> pdb=" O LYS D 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.555A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 216 through 220 removed outlier: 3.525A pdb=" N ASP E 219 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU E 220 " --> pdb=" O SER E 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 216 through 220' Processing helix chain 'E' and resid 385 through 392 removed outlier: 3.615A pdb=" N LEU E 389 " --> pdb=" O SER E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 452 removed outlier: 4.222A pdb=" N GLU E 451 " --> pdb=" O LYS E 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.554A pdb=" N ASP F 90 " --> pdb=" O ARG F 87 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 87 through 91' Processing helix chain 'F' and resid 216 through 220 removed outlier: 3.526A pdb=" N ASP F 219 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 220 " --> pdb=" O SER F 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 216 through 220' Processing helix chain 'F' and resid 385 through 392 removed outlier: 3.616A pdb=" N LEU F 389 " --> pdb=" O SER F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 452 removed outlier: 4.222A pdb=" N GLU F 451 " --> pdb=" O LYS F 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.680A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 170 through 172 No H-bonds generated for 'chain 'G' and resid 170 through 172' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.681A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 170 through 172 No H-bonds generated for 'chain 'I' and resid 170 through 172' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.167A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.243A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.828A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.535A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 105 through 106 removed outlier: 7.048A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.990A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.298A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 105 through 106 Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.252A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 324 through 328 removed outlier: 7.090A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB3, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.553A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.618A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 659 through 660 removed outlier: 3.999A pdb=" N TYR A 660 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.543A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.677A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.155A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.265A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.471A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.035A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.851A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.605A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 101 through 103 removed outlier: 3.903A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.802A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.355A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 324 through 326 removed outlier: 7.280A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.909A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.529A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 565 through 567 Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.339A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.430A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.706A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.245A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.250A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.549A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.351A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.795A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE9, first strand: chain 'C' and resid 116 through 121 Processing sheet with id=AF1, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AF2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.314A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AF4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.811A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.553A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.373A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AF9, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.196A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.267A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.466A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG4, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 145 through 148 removed outlier: 3.849A pdb=" N ALA D 146 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 153 through 157 Processing sheet with id=AG9, first strand: chain 'D' and resid 182 through 185 removed outlier: 6.333A pdb=" N TRP D 172 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 272 through 273 Processing sheet with id=AH2, first strand: chain 'D' and resid 278 through 284 Processing sheet with id=AH3, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.308A pdb=" N TRP D 297 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.308A pdb=" N TRP D 297 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 378 through 382 removed outlier: 3.530A pdb=" N VAL D 397 " --> pdb=" O PHE D 382 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR D 437 " --> pdb=" O ASN D 402 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER D 440 " --> pdb=" O SER D 426 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 409 through 411 Processing sheet with id=AH7, first strand: chain 'D' and resid 455 through 456 removed outlier: 3.526A pdb=" N TYR D 456 " --> pdb=" O PHE D 473 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 473 " --> pdb=" O TYR D 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AH9, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.654A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.654A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 145 through 148 removed outlier: 3.848A pdb=" N ALA E 146 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 153 through 157 Processing sheet with id=AI4, first strand: chain 'E' and resid 182 through 185 removed outlier: 6.333A pdb=" N TRP E 172 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 272 through 273 Processing sheet with id=AI6, first strand: chain 'E' and resid 278 through 284 Processing sheet with id=AI7, first strand: chain 'E' and resid 307 through 310 removed outlier: 6.306A pdb=" N TRP E 297 " --> pdb=" O LEU E 309 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 307 through 310 removed outlier: 6.306A pdb=" N TRP E 297 " --> pdb=" O LEU E 309 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 378 through 382 removed outlier: 3.530A pdb=" N VAL E 397 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR E 437 " --> pdb=" O ASN E 402 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER E 440 " --> pdb=" O SER E 426 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 409 through 411 Processing sheet with id=AJ2, first strand: chain 'E' and resid 455 through 456 removed outlier: 3.526A pdb=" N TYR E 456 " --> pdb=" O PHE E 473 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE E 473 " --> pdb=" O TYR E 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AJ4, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.654A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR F 110 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.654A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 145 through 148 removed outlier: 3.848A pdb=" N ALA F 146 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'F' and resid 153 through 157 Processing sheet with id=AJ8, first strand: chain 'F' and resid 182 through 185 removed outlier: 6.332A pdb=" N TRP F 172 " --> pdb=" O LEU F 184 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'F' and resid 272 through 273 Processing sheet with id=AK1, first strand: chain 'F' and resid 278 through 284 Processing sheet with id=AK2, first strand: chain 'F' and resid 307 through 310 removed outlier: 6.307A pdb=" N TRP F 297 " --> pdb=" O LEU F 309 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'F' and resid 378 through 382 removed outlier: 3.529A pdb=" N VAL F 397 " --> pdb=" O PHE F 382 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR F 437 " --> pdb=" O ASN F 402 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER F 440 " --> pdb=" O SER F 426 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'F' and resid 409 through 411 Processing sheet with id=AK5, first strand: chain 'F' and resid 455 through 456 removed outlier: 3.527A pdb=" N TYR F 456 " --> pdb=" O PHE F 473 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE F 473 " --> pdb=" O TYR F 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK5 Processing sheet with id=AK6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AK7, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.848A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.677A pdb=" N VAL G 116 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'G' and resid 134 through 137 removed outlier: 3.828A pdb=" N LEU G 152 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TYR G 190 " --> pdb=" O ASP G 158 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'G' and resid 165 through 168 Processing sheet with id=AL2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AL3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.843A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.680A pdb=" N VAL H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'H' and resid 134 through 138 removed outlier: 4.308A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU H 152 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'H' and resid 165 through 168 Processing sheet with id=AL7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AL8, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.847A pdb=" N MET I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TRP I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.680A pdb=" N VAL I 116 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'I' and resid 134 through 138 removed outlier: 4.310A pdb=" N GLY I 153 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU I 152 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR I 190 " --> pdb=" O ASP I 158 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'I' and resid 165 through 168 1559 hydrogen bonds defined for protein. 4095 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: 21.84 Time building geometry restraints manager: 17.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11584 1.33 - 1.46: 8105 1.46 - 1.58: 20152 1.58 - 1.70: 0 1.70 - 1.82: 198 Bond restraints: 40039 Sorted by residual: bond pdb=" N ILE G 101 " pdb=" CA ILE G 101 " ideal model delta sigma weight residual 1.459 1.495 -0.037 9.10e-03 1.21e+04 1.61e+01 bond pdb=" CA PRO A 25 " pdb=" C PRO A 25 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.58e+01 bond pdb=" N ILE H 101 " pdb=" CA ILE H 101 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.30e-03 1.16e+04 1.55e+01 bond pdb=" N ILE I 101 " pdb=" CA ILE I 101 " ideal model delta sigma weight residual 1.457 1.493 -0.036 9.30e-03 1.16e+04 1.49e+01 bond pdb=" N VAL C 213 " pdb=" CA VAL C 213 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.30e+01 ... (remaining 40034 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.35: 1141 106.35 - 113.35: 21789 113.35 - 120.35: 14554 120.35 - 127.34: 16676 127.34 - 134.34: 328 Bond angle restraints: 54488 Sorted by residual: angle pdb=" C ASN B 544 " pdb=" CA ASN B 544 " pdb=" CB ASN B 544 " ideal model delta sigma weight residual 116.54 109.82 6.72 1.15e+00 7.56e-01 3.41e+01 angle pdb=" C ASN A 331 " pdb=" CA ASN A 331 " pdb=" CB ASN A 331 " ideal model delta sigma weight residual 109.84 118.28 -8.44 1.50e+00 4.44e-01 3.17e+01 angle pdb=" N MET G 114 " pdb=" CA MET G 114 " pdb=" C MET G 114 " ideal model delta sigma weight residual 109.15 101.69 7.46 1.44e+00 4.82e-01 2.68e+01 angle pdb=" N PHE B 456 " pdb=" CA PHE B 456 " pdb=" C PHE B 456 " ideal model delta sigma weight residual 108.02 117.05 -9.03 1.75e+00 3.27e-01 2.66e+01 angle pdb=" N MET H 114 " pdb=" CA MET H 114 " pdb=" C MET H 114 " ideal model delta sigma weight residual 109.15 101.82 7.33 1.44e+00 4.82e-01 2.59e+01 ... (remaining 54483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 21841 17.92 - 35.83: 1891 35.83 - 53.75: 360 53.75 - 71.66: 78 71.66 - 89.58: 43 Dihedral angle restraints: 24213 sinusoidal: 9705 harmonic: 14508 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -157.25 71.25 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -157.23 71.23 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -157.19 71.19 1 1.00e+01 1.00e-02 6.51e+01 ... (remaining 24210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.237: 6222 0.237 - 0.473: 12 0.473 - 0.710: 4 0.710 - 0.947: 2 0.947 - 1.184: 1 Chirality restraints: 6241 Sorted by residual: chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.22 -1.18 2.00e-01 2.50e+01 3.50e+01 chirality pdb=" C1 NAG C1405 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1405 " pdb=" O5 NAG C1405 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C1 NAG C1402 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1402 " pdb=" O5 NAG C1402 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 ... (remaining 6238 not shown) Planarity restraints: 7033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " 0.353 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG B1309 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " 0.103 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1402 " 0.354 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C1402 " -0.090 2.00e-02 2.50e+03 pdb=" C8 NAG C1402 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG C1402 " -0.532 2.00e-02 2.50e+03 pdb=" O7 NAG C1402 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1408 " 0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG C1408 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1408 " 0.064 2.00e-02 2.50e+03 pdb=" N2 NAG C1408 " -0.525 2.00e-02 2.50e+03 pdb=" O7 NAG C1408 " 0.196 2.00e-02 2.50e+03 ... (remaining 7030 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 6083 2.76 - 3.29: 39350 3.29 - 3.83: 66571 3.83 - 4.36: 82445 4.36 - 4.90: 139124 Nonbonded interactions: 333573 Sorted by model distance: nonbonded pdb=" OH TYR E 173 " pdb=" OH TYR E 235 " model vdw 2.222 2.440 nonbonded pdb=" OH TYR F 173 " pdb=" OH TYR F 235 " model vdw 2.222 2.440 nonbonded pdb=" OH TYR D 173 " pdb=" OH TYR D 235 " model vdw 2.223 2.440 nonbonded pdb=" OH TYR E 298 " pdb=" OH TYR E 360 " model vdw 2.223 2.440 nonbonded pdb=" OH TYR D 298 " pdb=" OH TYR D 360 " model vdw 2.224 2.440 ... (remaining 333568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 1148 or resid 1301 through 1310)) selection = (chain 'B' and (resid 16 through 1148 or resid 1301 through 1310)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 15.740 Check model and map are aligned: 0.650 Set scattering table: 0.400 Process input model: 112.100 Find NCS groups from input model: 2.630 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4227 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 : 0.006 0.048 40039 Z= 0.402 Angle : 0.834 10.077 54488 Z= 0.515 Chirality : 0.061 1.184 6241 Planarity : 0.015 0.305 7004 Dihedral : 14.001 89.576 14748 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.78 % Allowed : 10.66 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.12), residues: 4938 helix: 0.16 (0.19), residues: 733 sheet: -1.03 (0.14), residues: 1272 loop : -1.25 (0.11), residues: 2933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 886 HIS 0.006 0.001 HIS B1048 PHE 0.029 0.002 PHE C 168 TYR 0.044 0.002 TYR B 904 ARG 0.012 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 586 time to evaluate : 3.979 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: A 188 ASN cc_start: 0.6694 (m-40) cc_final: 0.5803 (p0) REVERT: A 314 GLN cc_start: 0.8147 (tt0) cc_final: 0.7793 (tp40) REVERT: A 319 ARG cc_start: 0.7573 (ptp90) cc_final: 0.6232 (ptm-80) REVERT: A 554 GLU cc_start: 0.8154 (pt0) cc_final: 0.7772 (mt-10) REVERT: A 663 ASP cc_start: 0.7549 (t0) cc_final: 0.7322 (t0) REVERT: A 775 ASP cc_start: 0.7420 (m-30) cc_final: 0.6923 (m-30) REVERT: A 787 GLN cc_start: 0.7928 (mt0) cc_final: 0.7138 (mt0) REVERT: A 796 ASP cc_start: 0.7267 (p0) cc_final: 0.6708 (t70) REVERT: A 875 SER cc_start: 0.7780 (t) cc_final: 0.7366 (p) REVERT: A 886 TRP cc_start: 0.6844 (p90) cc_final: 0.6033 (p90) REVERT: A 919 ASN cc_start: 0.7083 (m-40) cc_final: 0.6870 (m110) REVERT: A 921 LYS cc_start: 0.6758 (mtpp) cc_final: 0.6484 (tttt) REVERT: A 985 ASP cc_start: 0.5820 (m-30) cc_final: 0.5441 (t0) REVERT: A 1017 GLU cc_start: 0.6657 (tt0) cc_final: 0.6438 (tt0) REVERT: A 1045 LYS cc_start: 0.7597 (mmmt) cc_final: 0.7191 (tptp) REVERT: A 1136 THR cc_start: 0.8446 (m) cc_final: 0.8230 (t) REVERT: B 48 LEU cc_start: 0.8414 (mt) cc_final: 0.8109 (mt) REVERT: B 191 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7716 (mt-10) REVERT: B 271 GLN cc_start: 0.7096 (mt0) cc_final: 0.6709 (mt0) REVERT: B 314 GLN cc_start: 0.8065 (tt0) cc_final: 0.7532 (tm-30) REVERT: B 675 GLN cc_start: 0.7211 (mt0) cc_final: 0.6604 (mt0) REVERT: B 790 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8073 (mtpp) REVERT: B 804 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7913 (mm-40) REVERT: B 875 SER cc_start: 0.8039 (t) cc_final: 0.7376 (m) REVERT: B 964 LYS cc_start: 0.7543 (mmtp) cc_final: 0.6952 (mptt) REVERT: B 1138 TYR cc_start: 0.6970 (t80) cc_final: 0.6586 (t80) REVERT: C 202 LYS cc_start: 0.6633 (mttm) cc_final: 0.6320 (mttp) REVERT: C 314 GLN cc_start: 0.8430 (tt0) cc_final: 0.8226 (tt0) REVERT: C 554 GLU cc_start: 0.8099 (pt0) cc_final: 0.7852 (pt0) REVERT: C 583 GLU cc_start: 0.7182 (tt0) cc_final: 0.6954 (tt0) REVERT: C 661 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6681 (mm-30) REVERT: C 675 GLN cc_start: 0.7091 (mt0) cc_final: 0.6822 (mt0) REVERT: C 790 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7915 (mtpp) REVERT: C 796 ASP cc_start: 0.8118 (t70) cc_final: 0.7043 (p0) REVERT: C 825 LYS cc_start: 0.7195 (mmtt) cc_final: 0.6966 (mptt) REVERT: C 867 ASP cc_start: 0.7478 (m-30) cc_final: 0.7212 (m-30) REVERT: C 875 SER cc_start: 0.7803 (t) cc_final: 0.7494 (p) REVERT: C 921 LYS cc_start: 0.6935 (mtpp) cc_final: 0.6410 (mmpt) REVERT: C 1045 LYS cc_start: 0.7856 (mmmt) cc_final: 0.7597 (tmtt) REVERT: C 1107 ARG cc_start: 0.7201 (mmt180) cc_final: 0.6669 (mmt90) REVERT: C 1119 ASN cc_start: 0.6807 (m-40) cc_final: 0.6293 (m-40) REVERT: D 156 LEU cc_start: -0.1523 (OUTLIER) cc_final: -0.1760 (pt) REVERT: D 387 GLU cc_start: 0.2790 (OUTLIER) cc_final: 0.2376 (mt-10) REVERT: E 344 ASP cc_start: 0.1483 (m-30) cc_final: 0.1212 (t70) outliers start: 34 outliers final: 7 residues processed: 613 average time/residue: 0.5121 time to fit residues: 509.0859 Evaluate side-chains 345 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 336 time to evaluate : 4.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain I residue 156 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 420 optimal weight: 30.0000 chunk 377 optimal weight: 20.0000 chunk 209 optimal weight: 3.9990 chunk 128 optimal weight: 0.0040 chunk 254 optimal weight: 0.5980 chunk 201 optimal weight: 0.5980 chunk 390 optimal weight: 40.0000 chunk 151 optimal weight: 0.3980 chunk 237 optimal weight: 10.0000 chunk 290 optimal weight: 2.9990 chunk 452 optimal weight: 7.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 354 ASN A 580 GLN A 616 ASN A 762 GLN A 901 GLN A 955 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN B 125 ASN B 196 ASN B 354 ASN B 493 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN B 955 ASN B1054 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 134 GLN C 196 ASN C 354 ASN C 493 GLN C 544 ASN C 764 ASN C 901 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN D 388 GLN D 416 ASN E 164 ASN E 358 ASN E 388 GLN F 277 GLN F 289 ASN F 388 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4292 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 40039 Z= 0.245 Angle : 0.649 10.682 54488 Z= 0.324 Chirality : 0.047 0.401 6241 Planarity : 0.005 0.071 7004 Dihedral : 5.761 53.344 6076 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.61 % Allowed : 12.35 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.12), residues: 4938 helix: 0.24 (0.19), residues: 737 sheet: -0.94 (0.13), residues: 1352 loop : -1.08 (0.12), residues: 2849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 111 HIS 0.004 0.001 HIS B 49 PHE 0.022 0.002 PHE E 29 TYR 0.037 0.001 TYR B 904 ARG 0.007 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 390 time to evaluate : 4.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.6467 (t0) cc_final: 0.6187 (t0) REVERT: A 54 LEU cc_start: 0.7130 (mp) cc_final: 0.6694 (mp) REVERT: A 117 LEU cc_start: 0.6048 (mp) cc_final: 0.5609 (tp) REVERT: A 188 ASN cc_start: 0.6810 (m-40) cc_final: 0.6076 (p0) REVERT: A 269 TYR cc_start: 0.7369 (m-80) cc_final: 0.6875 (m-80) REVERT: A 314 GLN cc_start: 0.8164 (tt0) cc_final: 0.7787 (tp40) REVERT: A 319 ARG cc_start: 0.7639 (ptp90) cc_final: 0.6447 (ptm160) REVERT: A 554 GLU cc_start: 0.8169 (pt0) cc_final: 0.7700 (mt-10) REVERT: A 565 PHE cc_start: 0.5654 (m-10) cc_final: 0.5277 (m-10) REVERT: A 584 ILE cc_start: 0.8396 (mm) cc_final: 0.7805 (mm) REVERT: A 775 ASP cc_start: 0.7205 (m-30) cc_final: 0.6942 (m-30) REVERT: A 787 GLN cc_start: 0.7923 (mt0) cc_final: 0.7700 (mm-40) REVERT: A 886 TRP cc_start: 0.6884 (p90) cc_final: 0.6117 (p90) REVERT: A 919 ASN cc_start: 0.7759 (m-40) cc_final: 0.7355 (m110) REVERT: A 921 LYS cc_start: 0.6786 (mtpp) cc_final: 0.6476 (tttt) REVERT: A 1017 GLU cc_start: 0.6772 (tt0) cc_final: 0.6529 (tt0) REVERT: A 1045 LYS cc_start: 0.7672 (mmmt) cc_final: 0.7101 (tmtt) REVERT: A 1114 ILE cc_start: 0.8709 (mt) cc_final: 0.8346 (mm) REVERT: A 1136 THR cc_start: 0.8526 (m) cc_final: 0.8297 (t) REVERT: B 191 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7545 (mt-10) REVERT: B 200 TYR cc_start: 0.6408 (t80) cc_final: 0.6169 (t80) REVERT: B 271 GLN cc_start: 0.7426 (mt0) cc_final: 0.6927 (mt0) REVERT: B 314 GLN cc_start: 0.8107 (tt0) cc_final: 0.7874 (tt0) REVERT: B 675 GLN cc_start: 0.7108 (mt0) cc_final: 0.6639 (mt0) REVERT: B 790 LYS cc_start: 0.8497 (mtpp) cc_final: 0.8128 (mtpp) REVERT: B 868 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6501 (mp0) REVERT: B 875 SER cc_start: 0.8173 (t) cc_final: 0.7516 (m) REVERT: B 886 TRP cc_start: 0.7245 (p90) cc_final: 0.6960 (p90) REVERT: B 983 ARG cc_start: 0.7813 (ptt180) cc_final: 0.7608 (ptm-80) REVERT: B 985 ASP cc_start: 0.6901 (OUTLIER) cc_final: 0.6385 (p0) REVERT: B 1017 GLU cc_start: 0.6758 (tp30) cc_final: 0.5953 (tt0) REVERT: B 1138 TYR cc_start: 0.6993 (t80) cc_final: 0.6642 (t80) REVERT: C 28 TYR cc_start: 0.7472 (m-80) cc_final: 0.6850 (m-80) REVERT: C 202 LYS cc_start: 0.6626 (mttm) cc_final: 0.6310 (mttp) REVERT: C 281 GLU cc_start: 0.8237 (pt0) cc_final: 0.7939 (pm20) REVERT: C 314 GLN cc_start: 0.8450 (tt0) cc_final: 0.8249 (tt0) REVERT: C 554 GLU cc_start: 0.8074 (pt0) cc_final: 0.7798 (pt0) REVERT: C 574 ASP cc_start: 0.7254 (t0) cc_final: 0.6996 (t0) REVERT: C 580 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6598 (pt0) REVERT: C 583 GLU cc_start: 0.7250 (tt0) cc_final: 0.6996 (tt0) REVERT: C 661 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6703 (mm-30) REVERT: C 675 GLN cc_start: 0.7029 (mt0) cc_final: 0.6732 (mt0) REVERT: C 790 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7904 (mtpp) REVERT: C 796 ASP cc_start: 0.8131 (t70) cc_final: 0.7058 (p0) REVERT: C 867 ASP cc_start: 0.7462 (m-30) cc_final: 0.7205 (m-30) REVERT: C 868 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6104 (mp0) REVERT: C 875 SER cc_start: 0.7926 (t) cc_final: 0.7611 (p) REVERT: C 1002 GLN cc_start: 0.6862 (tt0) cc_final: 0.6629 (tt0) REVERT: C 1006 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8147 (m) REVERT: C 1045 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7629 (tmtt) REVERT: C 1107 ARG cc_start: 0.7343 (mmt180) cc_final: 0.7106 (mmt180) REVERT: C 1116 THR cc_start: 0.7732 (p) cc_final: 0.7294 (p) REVERT: C 1119 ASN cc_start: 0.6847 (m-40) cc_final: 0.6351 (m-40) REVERT: D 387 GLU cc_start: 0.3528 (OUTLIER) cc_final: 0.2895 (mt-10) REVERT: E 216 ARG cc_start: 0.3647 (mmt-90) cc_final: 0.3305 (mmt-90) REVERT: E 230 TYR cc_start: 0.3036 (p90) cc_final: 0.2348 (p90) REVERT: E 344 ASP cc_start: 0.1587 (m-30) cc_final: 0.1320 (t70) REVERT: F 153 ARG cc_start: 0.3998 (ttp80) cc_final: 0.3042 (mtt180) REVERT: F 314 ASN cc_start: 0.5238 (t0) cc_final: 0.4807 (m110) REVERT: F 440 SER cc_start: 0.1705 (OUTLIER) cc_final: 0.1428 (t) REVERT: H 114 MET cc_start: 0.1630 (tpt) cc_final: 0.1386 (tpp) outliers start: 113 outliers final: 59 residues processed: 479 average time/residue: 0.5104 time to fit residues: 416.4310 Evaluate side-chains 401 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 337 time to evaluate : 4.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 440 SER Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain I residue 156 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 251 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 376 optimal weight: 50.0000 chunk 307 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 453 optimal weight: 40.0000 chunk 489 optimal weight: 30.0000 chunk 403 optimal weight: 10.0000 chunk 449 optimal weight: 10.0000 chunk 154 optimal weight: 0.7980 chunk 363 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 360 ASN A 493 GLN A 613 GLN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 493 GLN B1083 HIS B1101 HIS C 99 ASN C 121 ASN C1002 GLN C1010 GLN C1071 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN ** F 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4383 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 40039 Z= 0.458 Angle : 0.688 11.233 54488 Z= 0.350 Chirality : 0.050 0.495 6241 Planarity : 0.005 0.076 7004 Dihedral : 5.844 57.908 6064 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.42 % Allowed : 13.71 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.12), residues: 4938 helix: -0.11 (0.18), residues: 728 sheet: -0.83 (0.13), residues: 1368 loop : -1.15 (0.12), residues: 2842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 412 HIS 0.005 0.001 HIS A 49 PHE 0.026 0.002 PHE B 374 TYR 0.031 0.002 TYR B 904 ARG 0.006 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 342 time to evaluate : 4.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6832 (m-90) cc_final: 0.6601 (m-90) REVERT: A 117 LEU cc_start: 0.5927 (mp) cc_final: 0.5509 (tp) REVERT: A 188 ASN cc_start: 0.6899 (m-40) cc_final: 0.6191 (p0) REVERT: A 314 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7655 (tp40) REVERT: A 319 ARG cc_start: 0.7598 (ptp90) cc_final: 0.6549 (ptm160) REVERT: A 553 THR cc_start: 0.6371 (m) cc_final: 0.6027 (p) REVERT: A 554 GLU cc_start: 0.8335 (pt0) cc_final: 0.7725 (mt-10) REVERT: A 584 ILE cc_start: 0.8509 (mm) cc_final: 0.7828 (mm) REVERT: A 613 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7639 (mt0) REVERT: A 787 GLN cc_start: 0.8008 (mt0) cc_final: 0.7267 (mt0) REVERT: A 886 TRP cc_start: 0.6974 (p90) cc_final: 0.6737 (p90) REVERT: A 904 TYR cc_start: 0.6515 (t80) cc_final: 0.6026 (t80) REVERT: A 921 LYS cc_start: 0.6779 (mtpp) cc_final: 0.6532 (tttp) REVERT: A 1017 GLU cc_start: 0.6828 (tt0) cc_final: 0.6497 (tt0) REVERT: A 1045 LYS cc_start: 0.7791 (mmmt) cc_final: 0.7316 (tmtt) REVERT: B 92 PHE cc_start: 0.6559 (t80) cc_final: 0.6142 (t80) REVERT: B 191 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7602 (mt-10) REVERT: B 271 GLN cc_start: 0.7486 (mt0) cc_final: 0.6980 (mt0) REVERT: B 586 ASP cc_start: 0.7524 (m-30) cc_final: 0.7322 (m-30) REVERT: B 675 GLN cc_start: 0.6965 (mt0) cc_final: 0.6394 (mt0) REVERT: B 790 LYS cc_start: 0.8506 (mtpp) cc_final: 0.8083 (mtpp) REVERT: B 868 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6445 (mp0) REVERT: B 983 ARG cc_start: 0.7778 (ptt180) cc_final: 0.7545 (ptm-80) REVERT: B 985 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.6345 (p0) REVERT: B 1017 GLU cc_start: 0.6766 (tp30) cc_final: 0.5926 (tt0) REVERT: B 1101 HIS cc_start: 0.7447 (m170) cc_final: 0.7152 (m-70) REVERT: B 1138 TYR cc_start: 0.7165 (t80) cc_final: 0.6880 (t80) REVERT: C 104 TRP cc_start: 0.6655 (m-90) cc_final: 0.6425 (m-90) REVERT: C 202 LYS cc_start: 0.6983 (mttm) cc_final: 0.6574 (mttp) REVERT: C 314 GLN cc_start: 0.8465 (tt0) cc_final: 0.8206 (tt0) REVERT: C 318 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7045 (p90) REVERT: C 554 GLU cc_start: 0.8192 (pt0) cc_final: 0.7980 (pt0) REVERT: C 580 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7154 (pt0) REVERT: C 661 GLU cc_start: 0.7652 (mt-10) cc_final: 0.6822 (mm-30) REVERT: C 675 GLN cc_start: 0.7006 (mt0) cc_final: 0.6765 (mt0) REVERT: C 790 LYS cc_start: 0.8264 (mtpp) cc_final: 0.7850 (mtpp) REVERT: C 823 PHE cc_start: 0.8208 (m-80) cc_final: 0.7937 (m-80) REVERT: C 868 GLU cc_start: 0.6516 (mm-30) cc_final: 0.5903 (mp0) REVERT: C 875 SER cc_start: 0.8052 (t) cc_final: 0.7658 (p) REVERT: C 1045 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7622 (tmtt) REVERT: C 1107 ARG cc_start: 0.7628 (mmt180) cc_final: 0.7283 (mmt180) REVERT: C 1119 ASN cc_start: 0.7502 (m-40) cc_final: 0.7054 (m-40) REVERT: D 387 GLU cc_start: 0.3568 (OUTLIER) cc_final: 0.2640 (pt0) REVERT: E 230 TYR cc_start: 0.3148 (p90) cc_final: 0.2489 (p90) REVERT: E 344 ASP cc_start: 0.1905 (m-30) cc_final: 0.1406 (t70) REVERT: F 153 ARG cc_start: 0.4331 (ttp80) cc_final: 0.3348 (mmt180) REVERT: F 451 GLU cc_start: 0.2373 (mp0) cc_final: 0.1461 (mt-10) outliers start: 148 outliers final: 88 residues processed: 449 average time/residue: 0.5008 time to fit residues: 384.4472 Evaluate side-chains 395 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 301 time to evaluate : 4.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 125 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 447 optimal weight: 6.9990 chunk 340 optimal weight: 30.0000 chunk 235 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 216 optimal weight: 7.9990 chunk 304 optimal weight: 0.8980 chunk 454 optimal weight: 50.0000 chunk 481 optimal weight: 20.0000 chunk 237 optimal weight: 10.0000 chunk 430 optimal weight: 40.0000 chunk 129 optimal weight: 2.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 613 GLN A 616 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 52 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN E 164 ASN F 101 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4450 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.098 40039 Z= 0.645 Angle : 0.762 10.557 54488 Z= 0.388 Chirality : 0.053 0.424 6241 Planarity : 0.006 0.061 7004 Dihedral : 6.234 58.303 6063 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.29 % Allowed : 15.19 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.11), residues: 4938 helix: -0.84 (0.17), residues: 764 sheet: -0.79 (0.13), residues: 1385 loop : -1.31 (0.12), residues: 2789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 886 HIS 0.007 0.002 HIS B1048 PHE 0.030 0.003 PHE A 43 TYR 0.026 0.002 TYR B 265 ARG 0.013 0.001 ARG F 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 309 time to evaluate : 4.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7012 (m-40) cc_final: 0.6220 (p0) REVERT: A 239 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.6729 (tm-30) REVERT: A 281 GLU cc_start: 0.8295 (pt0) cc_final: 0.7942 (pm20) REVERT: A 314 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7553 (tp40) REVERT: A 319 ARG cc_start: 0.7554 (ptp90) cc_final: 0.6508 (ptm160) REVERT: A 553 THR cc_start: 0.6506 (m) cc_final: 0.6177 (p) REVERT: A 554 GLU cc_start: 0.8492 (pt0) cc_final: 0.7840 (mt-10) REVERT: A 740 MET cc_start: 0.7641 (tpp) cc_final: 0.7350 (ttt) REVERT: A 756 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.6051 (t80) REVERT: A 787 GLN cc_start: 0.8141 (mt0) cc_final: 0.7498 (mt0) REVERT: A 886 TRP cc_start: 0.6870 (p90) cc_final: 0.6390 (p90) REVERT: A 921 LYS cc_start: 0.6919 (mtpp) cc_final: 0.6616 (tttp) REVERT: A 935 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6856 (tp-100) REVERT: A 1002 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7701 (tm-30) REVERT: A 1017 GLU cc_start: 0.6959 (tt0) cc_final: 0.6742 (tt0) REVERT: A 1045 LYS cc_start: 0.7849 (mmmt) cc_final: 0.7450 (tmtt) REVERT: B 271 GLN cc_start: 0.7626 (mt0) cc_final: 0.7112 (mt0) REVERT: B 614 ASP cc_start: 0.4620 (m-30) cc_final: 0.4363 (m-30) REVERT: B 675 GLN cc_start: 0.6996 (mt0) cc_final: 0.6325 (mt0) REVERT: B 790 LYS cc_start: 0.8479 (mtpp) cc_final: 0.8075 (mtpp) REVERT: B 825 LYS cc_start: 0.6992 (mmtt) cc_final: 0.6470 (mptt) REVERT: B 868 GLU cc_start: 0.7419 (tm-30) cc_final: 0.6470 (mp0) REVERT: B 985 ASP cc_start: 0.6663 (OUTLIER) cc_final: 0.6278 (p0) REVERT: B 1017 GLU cc_start: 0.6773 (tp30) cc_final: 0.5944 (tt0) REVERT: B 1101 HIS cc_start: 0.7738 (m170) cc_final: 0.7507 (m-70) REVERT: C 117 LEU cc_start: 0.5736 (mp) cc_final: 0.5520 (tp) REVERT: C 202 LYS cc_start: 0.7215 (mttm) cc_final: 0.6986 (mtmm) REVERT: C 293 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6598 (pt) REVERT: C 314 GLN cc_start: 0.8464 (tt0) cc_final: 0.8109 (tt0) REVERT: C 318 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.6963 (p90) REVERT: C 554 GLU cc_start: 0.8120 (pt0) cc_final: 0.7915 (pt0) REVERT: C 661 GLU cc_start: 0.7678 (mt-10) cc_final: 0.6716 (mm-30) REVERT: C 675 GLN cc_start: 0.6901 (mt0) cc_final: 0.6683 (mt0) REVERT: C 790 LYS cc_start: 0.8253 (mtpp) cc_final: 0.7875 (mtpp) REVERT: C 811 LYS cc_start: 0.6178 (mtmt) cc_final: 0.5763 (ptpt) REVERT: C 868 GLU cc_start: 0.6454 (mm-30) cc_final: 0.5805 (mp0) REVERT: C 875 SER cc_start: 0.8136 (t) cc_final: 0.7749 (p) REVERT: C 964 LYS cc_start: 0.7478 (ttmm) cc_final: 0.6935 (mmtt) REVERT: C 1005 GLN cc_start: 0.7673 (tp40) cc_final: 0.7305 (mm-40) REVERT: C 1045 LYS cc_start: 0.8014 (mmmt) cc_final: 0.7644 (tttt) REVERT: C 1107 ARG cc_start: 0.7672 (mmt180) cc_final: 0.7126 (mmt180) REVERT: C 1119 ASN cc_start: 0.7680 (m-40) cc_final: 0.7299 (m-40) REVERT: D 67 ARG cc_start: 0.2200 (ptp-170) cc_final: 0.1854 (mtt180) REVERT: D 113 GLN cc_start: 0.2543 (OUTLIER) cc_final: 0.2156 (pm20) REVERT: D 387 GLU cc_start: 0.3689 (OUTLIER) cc_final: 0.2710 (pt0) REVERT: E 36 TRP cc_start: 0.4978 (m100) cc_final: 0.4717 (m100) REVERT: E 230 TYR cc_start: 0.3028 (p90) cc_final: 0.2396 (p90) REVERT: F 34 MET cc_start: 0.4111 (mmp) cc_final: 0.3613 (mmm) REVERT: F 153 ARG cc_start: 0.4376 (ttp80) cc_final: 0.3350 (mmt180) REVERT: F 451 GLU cc_start: 0.2348 (mp0) cc_final: 0.1389 (mt-10) outliers start: 186 outliers final: 120 residues processed: 450 average time/residue: 0.4937 time to fit residues: 377.2167 Evaluate side-chains 414 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 285 time to evaluate : 4.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 432 SER Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 164 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 400 optimal weight: 10.0000 chunk 273 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 358 optimal weight: 8.9990 chunk 198 optimal weight: 0.5980 chunk 410 optimal weight: 0.9990 chunk 332 optimal weight: 20.0000 chunk 0 optimal weight: 10.9990 chunk 245 optimal weight: 8.9990 chunk 432 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 519 HIS A 580 GLN A 613 GLN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN F 277 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4388 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 40039 Z= 0.246 Angle : 0.590 9.693 54488 Z= 0.300 Chirality : 0.045 0.310 6241 Planarity : 0.004 0.052 7004 Dihedral : 5.744 56.717 6063 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.53 % Allowed : 16.46 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.12), residues: 4938 helix: -0.16 (0.18), residues: 739 sheet: -0.67 (0.13), residues: 1394 loop : -1.19 (0.12), residues: 2805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 297 HIS 0.003 0.001 HIS C1064 PHE 0.029 0.002 PHE D 29 TYR 0.022 0.001 TYR C 369 ARG 0.005 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 309 time to evaluate : 4.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6066 (mp) cc_final: 0.5628 (tp) REVERT: A 188 ASN cc_start: 0.6904 (m-40) cc_final: 0.6174 (p0) REVERT: A 314 GLN cc_start: 0.8206 (tt0) cc_final: 0.7925 (tp40) REVERT: A 319 ARG cc_start: 0.7524 (ptp90) cc_final: 0.6421 (ptm160) REVERT: A 541 PHE cc_start: 0.7221 (p90) cc_final: 0.6972 (p90) REVERT: A 554 GLU cc_start: 0.8513 (pt0) cc_final: 0.7858 (mt-10) REVERT: A 756 TYR cc_start: 0.6556 (OUTLIER) cc_final: 0.6161 (t80) REVERT: A 787 GLN cc_start: 0.8097 (mt0) cc_final: 0.7515 (mt0) REVERT: A 886 TRP cc_start: 0.6837 (p90) cc_final: 0.6280 (p90) REVERT: A 921 LYS cc_start: 0.6839 (mtpp) cc_final: 0.6557 (tttp) REVERT: A 995 ARG cc_start: 0.6587 (tpp80) cc_final: 0.6141 (mtm180) REVERT: A 1017 GLU cc_start: 0.6908 (tt0) cc_final: 0.6595 (tt0) REVERT: A 1045 LYS cc_start: 0.7843 (mmmt) cc_final: 0.7364 (tmtt) REVERT: B 92 PHE cc_start: 0.6700 (t80) cc_final: 0.6219 (t80) REVERT: B 271 GLN cc_start: 0.7686 (mt0) cc_final: 0.7213 (mt0) REVERT: B 675 GLN cc_start: 0.6931 (mt0) cc_final: 0.6220 (mt0) REVERT: B 790 LYS cc_start: 0.8471 (mtpp) cc_final: 0.8094 (mtpp) REVERT: B 868 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7169 (tt0) REVERT: B 985 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.6202 (p0) REVERT: B 1017 GLU cc_start: 0.6690 (tp30) cc_final: 0.5921 (tt0) REVERT: B 1101 HIS cc_start: 0.7798 (m170) cc_final: 0.7424 (m-70) REVERT: C 202 LYS cc_start: 0.7143 (mttm) cc_final: 0.6926 (mtmm) REVERT: C 293 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6593 (pt) REVERT: C 314 GLN cc_start: 0.8403 (tt0) cc_final: 0.8069 (tt0) REVERT: C 318 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7019 (p90) REVERT: C 661 GLU cc_start: 0.7618 (mt-10) cc_final: 0.6650 (mm-30) REVERT: C 675 GLN cc_start: 0.6885 (mt0) cc_final: 0.6653 (mt0) REVERT: C 790 LYS cc_start: 0.8234 (mtpp) cc_final: 0.7860 (mtpp) REVERT: C 811 LYS cc_start: 0.6052 (mtmt) cc_final: 0.5648 (ptpt) REVERT: C 868 GLU cc_start: 0.6197 (mm-30) cc_final: 0.5555 (mp0) REVERT: C 875 SER cc_start: 0.8115 (t) cc_final: 0.7779 (p) REVERT: C 886 TRP cc_start: 0.7226 (p90) cc_final: 0.6473 (p90) REVERT: C 1005 GLN cc_start: 0.7589 (tp40) cc_final: 0.7212 (mm-40) REVERT: C 1045 LYS cc_start: 0.8000 (mmmt) cc_final: 0.7595 (tttt) REVERT: C 1107 ARG cc_start: 0.7592 (mmt180) cc_final: 0.7118 (mmt180) REVERT: D 34 MET cc_start: 0.3363 (OUTLIER) cc_final: 0.2979 (mmm) REVERT: D 67 ARG cc_start: 0.2011 (ptp-170) cc_final: 0.1728 (mtt180) REVERT: D 324 PHE cc_start: 0.1652 (m-80) cc_final: 0.0502 (t80) REVERT: D 387 GLU cc_start: 0.3739 (OUTLIER) cc_final: 0.2701 (pt0) REVERT: E 230 TYR cc_start: 0.3001 (p90) cc_final: 0.2450 (p90) REVERT: F 34 MET cc_start: 0.4084 (mmp) cc_final: 0.3723 (mmm) REVERT: F 153 ARG cc_start: 0.4406 (ttp80) cc_final: 0.3289 (mmt180) REVERT: F 277 GLN cc_start: 0.1424 (OUTLIER) cc_final: 0.0054 (tp40) REVERT: F 451 GLU cc_start: 0.2335 (mp0) cc_final: 0.1509 (mt-10) REVERT: G 124 THR cc_start: 0.0465 (p) cc_final: -0.0153 (t) outliers start: 153 outliers final: 91 residues processed: 419 average time/residue: 0.4774 time to fit residues: 338.6203 Evaluate side-chains 383 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 285 time to evaluate : 4.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 125 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 161 optimal weight: 0.7980 chunk 433 optimal weight: 30.0000 chunk 95 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 481 optimal weight: 10.0000 chunk 399 optimal weight: 20.0000 chunk 223 optimal weight: 0.6980 chunk 40 optimal weight: 0.1980 chunk 159 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN F 277 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4383 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40039 Z= 0.230 Angle : 0.573 9.657 54488 Z= 0.290 Chirality : 0.044 0.365 6241 Planarity : 0.004 0.050 7004 Dihedral : 5.531 56.846 6063 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.42 % Allowed : 16.62 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.12), residues: 4938 helix: 0.10 (0.18), residues: 740 sheet: -0.58 (0.13), residues: 1400 loop : -1.11 (0.12), residues: 2798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP E 36 HIS 0.003 0.001 HIS C1064 PHE 0.026 0.002 PHE D 29 TYR 0.021 0.001 TYR C 369 ARG 0.018 0.000 ARG F 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 310 time to evaluate : 4.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6040 (mp) cc_final: 0.5581 (tp) REVERT: A 188 ASN cc_start: 0.6925 (m-40) cc_final: 0.6279 (p0) REVERT: A 239 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6382 (tm-30) REVERT: A 314 GLN cc_start: 0.8157 (tt0) cc_final: 0.7917 (tp40) REVERT: A 319 ARG cc_start: 0.7478 (ptp90) cc_final: 0.6346 (ptm160) REVERT: A 541 PHE cc_start: 0.7248 (p90) cc_final: 0.6941 (p90) REVERT: A 554 GLU cc_start: 0.8511 (pt0) cc_final: 0.7880 (mt-10) REVERT: A 756 TYR cc_start: 0.6508 (OUTLIER) cc_final: 0.6119 (t80) REVERT: A 787 GLN cc_start: 0.8109 (mt0) cc_final: 0.7557 (mt0) REVERT: A 811 LYS cc_start: 0.5555 (mttt) cc_final: 0.4983 (mptt) REVERT: A 886 TRP cc_start: 0.6801 (p90) cc_final: 0.6350 (p90) REVERT: A 921 LYS cc_start: 0.6836 (mtpp) cc_final: 0.6553 (tttp) REVERT: A 995 ARG cc_start: 0.6504 (tpp80) cc_final: 0.6081 (mtm180) REVERT: A 1017 GLU cc_start: 0.6935 (tt0) cc_final: 0.6681 (tt0) REVERT: A 1045 LYS cc_start: 0.7835 (mmmt) cc_final: 0.7360 (tmtt) REVERT: B 92 PHE cc_start: 0.6662 (t80) cc_final: 0.6193 (t80) REVERT: B 271 GLN cc_start: 0.7613 (mt0) cc_final: 0.7124 (mt0) REVERT: B 675 GLN cc_start: 0.6944 (mt0) cc_final: 0.6224 (mt0) REVERT: B 790 LYS cc_start: 0.8460 (mtpp) cc_final: 0.8043 (mtpp) REVERT: B 821 LEU cc_start: 0.6899 (tt) cc_final: 0.6683 (tt) REVERT: B 868 GLU cc_start: 0.7372 (tm-30) cc_final: 0.6383 (mp0) REVERT: B 917 TYR cc_start: 0.8396 (m-80) cc_final: 0.8047 (m-80) REVERT: B 985 ASP cc_start: 0.6641 (OUTLIER) cc_final: 0.6252 (p0) REVERT: B 1017 GLU cc_start: 0.6690 (tp30) cc_final: 0.5922 (tt0) REVERT: B 1101 HIS cc_start: 0.7823 (m170) cc_final: 0.7431 (m-70) REVERT: C 190 ARG cc_start: 0.6536 (mtt90) cc_final: 0.6331 (mtt180) REVERT: C 202 LYS cc_start: 0.7164 (mttm) cc_final: 0.6798 (mttp) REVERT: C 293 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6593 (pt) REVERT: C 314 GLN cc_start: 0.8398 (tt0) cc_final: 0.8061 (tt0) REVERT: C 318 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.6868 (p90) REVERT: C 661 GLU cc_start: 0.7539 (mt-10) cc_final: 0.6631 (mm-30) REVERT: C 675 GLN cc_start: 0.6890 (mt0) cc_final: 0.6633 (mt0) REVERT: C 790 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7867 (mtpp) REVERT: C 811 LYS cc_start: 0.6040 (mtmt) cc_final: 0.5641 (ptpt) REVERT: C 823 PHE cc_start: 0.7973 (m-80) cc_final: 0.7725 (m-80) REVERT: C 868 GLU cc_start: 0.6198 (mm-30) cc_final: 0.5575 (mp0) REVERT: C 875 SER cc_start: 0.8116 (t) cc_final: 0.7765 (p) REVERT: C 886 TRP cc_start: 0.7226 (p90) cc_final: 0.6477 (p90) REVERT: C 1005 GLN cc_start: 0.7605 (tp40) cc_final: 0.7213 (mm-40) REVERT: C 1045 LYS cc_start: 0.7987 (mmmt) cc_final: 0.7555 (tttt) REVERT: C 1107 ARG cc_start: 0.7552 (mmt180) cc_final: 0.7081 (mmt180) REVERT: D 34 MET cc_start: 0.3434 (OUTLIER) cc_final: 0.3002 (mmm) REVERT: D 67 ARG cc_start: 0.2016 (ptp-170) cc_final: 0.1726 (mtt180) REVERT: D 324 PHE cc_start: 0.1614 (m-80) cc_final: 0.0545 (t80) REVERT: E 190 GLN cc_start: 0.6042 (OUTLIER) cc_final: 0.4759 (mp10) REVERT: E 230 TYR cc_start: 0.2974 (p90) cc_final: 0.2443 (p90) REVERT: F 34 MET cc_start: 0.4027 (mmp) cc_final: 0.3690 (mmm) REVERT: F 153 ARG cc_start: 0.4404 (ttp80) cc_final: 0.3271 (mmt180) REVERT: F 277 GLN cc_start: 0.1439 (OUTLIER) cc_final: 0.0318 (tp40) REVERT: F 451 GLU cc_start: 0.2425 (mp0) cc_final: 0.1559 (mt-10) REVERT: G 122 LEU cc_start: 0.2640 (OUTLIER) cc_final: 0.2043 (tt) REVERT: G 124 THR cc_start: 0.0631 (p) cc_final: 0.0053 (t) REVERT: G 192 LEU cc_start: 0.2848 (OUTLIER) cc_final: 0.2471 (tp) REVERT: H 114 MET cc_start: 0.1571 (tpp) cc_final: 0.1034 (tpp) outliers start: 148 outliers final: 103 residues processed: 411 average time/residue: 0.4850 time to fit residues: 336.8672 Evaluate side-chains 403 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 290 time to evaluate : 5.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 122 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 464 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 274 optimal weight: 0.1980 chunk 351 optimal weight: 40.0000 chunk 272 optimal weight: 3.9990 chunk 405 optimal weight: 20.0000 chunk 269 optimal weight: 0.9980 chunk 479 optimal weight: 7.9990 chunk 300 optimal weight: 0.6980 chunk 292 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN D 101 ASN D 267 GLN D 388 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4403 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 40039 Z= 0.312 Angle : 0.590 9.702 54488 Z= 0.298 Chirality : 0.045 0.383 6241 Planarity : 0.004 0.052 7004 Dihedral : 5.486 56.609 6063 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.79 % Allowed : 16.69 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.12), residues: 4938 helix: 0.10 (0.18), residues: 740 sheet: -0.48 (0.13), residues: 1397 loop : -1.11 (0.12), residues: 2801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 36 HIS 0.003 0.001 HIS C1064 PHE 0.025 0.002 PHE D 29 TYR 0.034 0.001 TYR F 173 ARG 0.007 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 301 time to evaluate : 4.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6106 (mp) cc_final: 0.5647 (tp) REVERT: A 188 ASN cc_start: 0.7002 (m-40) cc_final: 0.6315 (p0) REVERT: A 239 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6331 (tm-30) REVERT: A 314 GLN cc_start: 0.8197 (tt0) cc_final: 0.7881 (tp40) REVERT: A 319 ARG cc_start: 0.7478 (ptp90) cc_final: 0.6304 (ptm160) REVERT: A 541 PHE cc_start: 0.7318 (p90) cc_final: 0.6955 (p90) REVERT: A 554 GLU cc_start: 0.8515 (pt0) cc_final: 0.7907 (mt-10) REVERT: A 584 ILE cc_start: 0.8332 (mm) cc_final: 0.7773 (mm) REVERT: A 756 TYR cc_start: 0.6492 (OUTLIER) cc_final: 0.6132 (t80) REVERT: A 787 GLN cc_start: 0.8135 (mt0) cc_final: 0.7573 (mt0) REVERT: A 886 TRP cc_start: 0.6780 (p90) cc_final: 0.6362 (p90) REVERT: A 921 LYS cc_start: 0.6952 (mtpp) cc_final: 0.6699 (tttp) REVERT: A 995 ARG cc_start: 0.6578 (tpp80) cc_final: 0.6128 (mtm180) REVERT: A 1017 GLU cc_start: 0.6936 (tt0) cc_final: 0.6701 (tt0) REVERT: A 1045 LYS cc_start: 0.7768 (mmmt) cc_final: 0.7297 (tmtt) REVERT: B 271 GLN cc_start: 0.7606 (mt0) cc_final: 0.7147 (mt0) REVERT: B 675 GLN cc_start: 0.6901 (mt0) cc_final: 0.6182 (mt0) REVERT: B 790 LYS cc_start: 0.8469 (mtpp) cc_final: 0.8030 (mtpp) REVERT: B 821 LEU cc_start: 0.6892 (tt) cc_final: 0.6651 (tp) REVERT: B 868 GLU cc_start: 0.7403 (tm-30) cc_final: 0.6402 (mp0) REVERT: B 985 ASP cc_start: 0.6628 (OUTLIER) cc_final: 0.6236 (p0) REVERT: B 1017 GLU cc_start: 0.6710 (tp30) cc_final: 0.5926 (tt0) REVERT: B 1101 HIS cc_start: 0.7890 (m170) cc_final: 0.7510 (m-70) REVERT: C 104 TRP cc_start: 0.6601 (m-90) cc_final: 0.6261 (m-90) REVERT: C 190 ARG cc_start: 0.6532 (mtt90) cc_final: 0.6313 (mtt180) REVERT: C 202 LYS cc_start: 0.7194 (mttm) cc_final: 0.6826 (mttp) REVERT: C 293 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6630 (pt) REVERT: C 314 GLN cc_start: 0.8442 (tt0) cc_final: 0.8116 (tt0) REVERT: C 318 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.6834 (p90) REVERT: C 661 GLU cc_start: 0.7598 (mt-10) cc_final: 0.6657 (mm-30) REVERT: C 675 GLN cc_start: 0.6838 (mt0) cc_final: 0.6631 (mt0) REVERT: C 790 LYS cc_start: 0.8262 (mtpp) cc_final: 0.7828 (mtpp) REVERT: C 811 LYS cc_start: 0.6115 (mtmt) cc_final: 0.5677 (ptpt) REVERT: C 868 GLU cc_start: 0.6198 (mm-30) cc_final: 0.5567 (mp0) REVERT: C 875 SER cc_start: 0.8116 (t) cc_final: 0.7759 (p) REVERT: C 886 TRP cc_start: 0.7275 (p90) cc_final: 0.6522 (p90) REVERT: C 1005 GLN cc_start: 0.7615 (tp40) cc_final: 0.7226 (mm-40) REVERT: C 1045 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7579 (tttt) REVERT: C 1107 ARG cc_start: 0.7568 (mmt180) cc_final: 0.7063 (mmt180) REVERT: D 34 MET cc_start: 0.3591 (OUTLIER) cc_final: 0.3124 (mmm) REVERT: D 67 ARG cc_start: 0.2036 (ptp-170) cc_final: 0.1749 (mtt180) REVERT: D 324 PHE cc_start: 0.1638 (m-80) cc_final: 0.0578 (t80) REVERT: E 81 LEU cc_start: 0.5207 (tp) cc_final: 0.4996 (tp) REVERT: E 190 GLN cc_start: 0.5972 (OUTLIER) cc_final: 0.4765 (mp10) REVERT: E 230 TYR cc_start: 0.3055 (p90) cc_final: 0.2497 (p90) REVERT: F 153 ARG cc_start: 0.4395 (ttp80) cc_final: 0.3253 (mmt90) REVERT: F 451 GLU cc_start: 0.2427 (mp0) cc_final: 0.1535 (mt-10) REVERT: G 122 LEU cc_start: 0.2322 (OUTLIER) cc_final: 0.1870 (tt) REVERT: G 124 THR cc_start: 0.0487 (p) cc_final: -0.0093 (t) REVERT: G 192 LEU cc_start: 0.2860 (OUTLIER) cc_final: 0.2522 (tp) REVERT: H 114 MET cc_start: 0.1549 (tpp) cc_final: 0.1101 (tpp) outliers start: 164 outliers final: 116 residues processed: 417 average time/residue: 0.4829 time to fit residues: 339.2198 Evaluate side-chains 412 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 287 time to evaluate : 4.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 122 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 296 optimal weight: 0.5980 chunk 191 optimal weight: 0.5980 chunk 286 optimal weight: 0.6980 chunk 144 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 305 optimal weight: 0.5980 chunk 327 optimal weight: 40.0000 chunk 237 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 377 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN F 164 ASN F 277 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4373 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 40039 Z= 0.188 Angle : 0.547 9.621 54488 Z= 0.276 Chirality : 0.043 0.378 6241 Planarity : 0.004 0.049 7004 Dihedral : 5.290 56.626 6063 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.82 % Allowed : 17.84 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.12), residues: 4938 helix: 0.43 (0.19), residues: 740 sheet: -0.37 (0.14), residues: 1377 loop : -1.01 (0.12), residues: 2821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 297 HIS 0.003 0.001 HIS A1048 PHE 0.025 0.001 PHE D 29 TYR 0.026 0.001 TYR F 298 ARG 0.006 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 314 time to evaluate : 4.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6100 (mp) cc_final: 0.5630 (tp) REVERT: A 188 ASN cc_start: 0.6982 (m-40) cc_final: 0.6313 (p0) REVERT: A 239 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6194 (tm-30) REVERT: A 314 GLN cc_start: 0.8151 (tt0) cc_final: 0.7880 (tp40) REVERT: A 319 ARG cc_start: 0.7501 (ptp90) cc_final: 0.6307 (ptm160) REVERT: A 541 PHE cc_start: 0.7215 (p90) cc_final: 0.6860 (p90) REVERT: A 554 GLU cc_start: 0.8512 (pt0) cc_final: 0.7910 (mt-10) REVERT: A 584 ILE cc_start: 0.8279 (mm) cc_final: 0.7725 (mm) REVERT: A 756 TYR cc_start: 0.6336 (OUTLIER) cc_final: 0.6109 (t80) REVERT: A 787 GLN cc_start: 0.8104 (mt0) cc_final: 0.7547 (mt0) REVERT: A 886 TRP cc_start: 0.6757 (p90) cc_final: 0.6335 (p90) REVERT: A 921 LYS cc_start: 0.6916 (mtpp) cc_final: 0.6635 (tttp) REVERT: A 995 ARG cc_start: 0.6472 (tpp80) cc_final: 0.6047 (mtm180) REVERT: A 1017 GLU cc_start: 0.7108 (tt0) cc_final: 0.6880 (tt0) REVERT: A 1045 LYS cc_start: 0.7705 (mmmt) cc_final: 0.7237 (tmtt) REVERT: B 271 GLN cc_start: 0.7616 (mt0) cc_final: 0.7142 (mt0) REVERT: B 673 SER cc_start: 0.8436 (t) cc_final: 0.8058 (p) REVERT: B 675 GLN cc_start: 0.6903 (mt0) cc_final: 0.6170 (mt0) REVERT: B 790 LYS cc_start: 0.8454 (mtpp) cc_final: 0.8033 (mtpp) REVERT: B 868 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6344 (mp0) REVERT: B 985 ASP cc_start: 0.6576 (OUTLIER) cc_final: 0.6259 (p0) REVERT: B 1017 GLU cc_start: 0.6675 (tp30) cc_final: 0.5922 (tt0) REVERT: B 1045 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7852 (mmmm) REVERT: B 1101 HIS cc_start: 0.7906 (m170) cc_final: 0.7475 (m-70) REVERT: C 104 TRP cc_start: 0.6500 (m-90) cc_final: 0.6060 (m-90) REVERT: C 190 ARG cc_start: 0.6580 (mtt90) cc_final: 0.6368 (mtt180) REVERT: C 202 LYS cc_start: 0.7145 (mttm) cc_final: 0.6803 (mttp) REVERT: C 237 ARG cc_start: 0.6268 (mtt180) cc_final: 0.5678 (mtp-110) REVERT: C 281 GLU cc_start: 0.8327 (pt0) cc_final: 0.7688 (pm20) REVERT: C 293 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6559 (pt) REVERT: C 314 GLN cc_start: 0.8325 (tt0) cc_final: 0.8012 (tt0) REVERT: C 318 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.6809 (p90) REVERT: C 661 GLU cc_start: 0.7522 (mt-10) cc_final: 0.6614 (mm-30) REVERT: C 790 LYS cc_start: 0.8271 (mtpp) cc_final: 0.7856 (mtpp) REVERT: C 811 LYS cc_start: 0.6154 (mtmt) cc_final: 0.5748 (ptpt) REVERT: C 823 PHE cc_start: 0.7920 (m-80) cc_final: 0.7684 (m-80) REVERT: C 868 GLU cc_start: 0.6171 (mm-30) cc_final: 0.5574 (mp0) REVERT: C 875 SER cc_start: 0.8112 (t) cc_final: 0.7754 (p) REVERT: C 886 TRP cc_start: 0.7260 (p90) cc_final: 0.6350 (p90) REVERT: C 995 ARG cc_start: 0.7000 (mtp85) cc_final: 0.6788 (mtp85) REVERT: C 1005 GLN cc_start: 0.7554 (tp40) cc_final: 0.7167 (mm-40) REVERT: C 1045 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7553 (tttt) REVERT: C 1107 ARG cc_start: 0.7473 (mmt180) cc_final: 0.7016 (mmt180) REVERT: D 34 MET cc_start: 0.3556 (OUTLIER) cc_final: 0.3257 (mmm) REVERT: D 67 ARG cc_start: 0.2001 (ptp-170) cc_final: 0.1728 (mtt180) REVERT: D 324 PHE cc_start: 0.1603 (m-80) cc_final: 0.0585 (t80) REVERT: E 190 GLN cc_start: 0.5900 (OUTLIER) cc_final: 0.4724 (mp10) REVERT: E 230 TYR cc_start: 0.3014 (p90) cc_final: 0.2483 (p90) REVERT: F 34 MET cc_start: 0.3922 (mmp) cc_final: 0.3307 (mmm) REVERT: F 153 ARG cc_start: 0.4359 (ttp80) cc_final: 0.3223 (mmt90) REVERT: F 277 GLN cc_start: 0.1488 (OUTLIER) cc_final: 0.1060 (tp40) REVERT: F 451 GLU cc_start: 0.2219 (mp0) cc_final: 0.1350 (mt-10) REVERT: G 122 LEU cc_start: 0.1930 (OUTLIER) cc_final: 0.1705 (tt) REVERT: G 124 THR cc_start: 0.0508 (p) cc_final: -0.0076 (t) REVERT: G 192 LEU cc_start: 0.2848 (OUTLIER) cc_final: 0.2546 (tp) REVERT: H 114 MET cc_start: 0.1562 (tpp) cc_final: 0.1200 (tpp) outliers start: 122 outliers final: 93 residues processed: 401 average time/residue: 0.4840 time to fit residues: 327.6184 Evaluate side-chains 405 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 301 time to evaluate : 4.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 432 SER Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 122 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 436 optimal weight: 10.0000 chunk 459 optimal weight: 50.0000 chunk 419 optimal weight: 20.0000 chunk 447 optimal weight: 0.5980 chunk 269 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 351 optimal weight: 40.0000 chunk 137 optimal weight: 0.9990 chunk 404 optimal weight: 0.8980 chunk 423 optimal weight: 7.9990 chunk 445 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4384 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 40039 Z= 0.233 Angle : 0.554 9.635 54488 Z= 0.279 Chirality : 0.044 0.301 6241 Planarity : 0.004 0.049 7004 Dihedral : 5.281 56.576 6063 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.98 % Allowed : 17.80 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 4938 helix: 0.47 (0.19), residues: 740 sheet: -0.28 (0.14), residues: 1376 loop : -1.00 (0.12), residues: 2822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 36 HIS 0.003 0.001 HIS C1064 PHE 0.027 0.001 PHE D 29 TYR 0.023 0.001 TYR C 369 ARG 0.010 0.000 ARG F 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 307 time to evaluate : 4.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6131 (mp) cc_final: 0.5661 (tp) REVERT: A 188 ASN cc_start: 0.6981 (m-40) cc_final: 0.6337 (p0) REVERT: A 239 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6253 (tm-30) REVERT: A 314 GLN cc_start: 0.8168 (tt0) cc_final: 0.7886 (tp40) REVERT: A 319 ARG cc_start: 0.7517 (ptp90) cc_final: 0.6315 (ptm160) REVERT: A 541 PHE cc_start: 0.7235 (p90) cc_final: 0.6820 (p90) REVERT: A 554 GLU cc_start: 0.8521 (pt0) cc_final: 0.7933 (mt-10) REVERT: A 756 TYR cc_start: 0.6371 (OUTLIER) cc_final: 0.6096 (t80) REVERT: A 787 GLN cc_start: 0.8122 (mt0) cc_final: 0.7551 (mt0) REVERT: A 811 LYS cc_start: 0.5592 (mttt) cc_final: 0.4993 (mptt) REVERT: A 886 TRP cc_start: 0.6748 (p90) cc_final: 0.6308 (p90) REVERT: A 918 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8124 (mp0) REVERT: A 921 LYS cc_start: 0.6945 (mtpp) cc_final: 0.6668 (tttp) REVERT: A 995 ARG cc_start: 0.6431 (tpp80) cc_final: 0.6008 (mtm180) REVERT: A 1017 GLU cc_start: 0.7116 (tt0) cc_final: 0.6891 (tt0) REVERT: A 1045 LYS cc_start: 0.7681 (mmmt) cc_final: 0.7212 (tmtt) REVERT: B 271 GLN cc_start: 0.7636 (mt0) cc_final: 0.7171 (mt0) REVERT: B 673 SER cc_start: 0.8430 (t) cc_final: 0.8067 (p) REVERT: B 675 GLN cc_start: 0.6913 (mt0) cc_final: 0.6186 (mt0) REVERT: B 790 LYS cc_start: 0.8457 (mtpp) cc_final: 0.8024 (mtpp) REVERT: B 868 GLU cc_start: 0.7400 (tm-30) cc_final: 0.6360 (mp0) REVERT: B 985 ASP cc_start: 0.6592 (OUTLIER) cc_final: 0.6257 (p0) REVERT: B 1017 GLU cc_start: 0.6700 (tp30) cc_final: 0.5923 (tt0) REVERT: B 1101 HIS cc_start: 0.7896 (m170) cc_final: 0.7474 (m-70) REVERT: C 104 TRP cc_start: 0.6567 (m-90) cc_final: 0.6121 (m-90) REVERT: C 190 ARG cc_start: 0.6585 (mtt90) cc_final: 0.6377 (mtt180) REVERT: C 202 LYS cc_start: 0.7137 (mttm) cc_final: 0.6795 (mttp) REVERT: C 237 ARG cc_start: 0.6279 (mtt180) cc_final: 0.5682 (mtp-110) REVERT: C 281 GLU cc_start: 0.8352 (pt0) cc_final: 0.7695 (pm20) REVERT: C 293 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6506 (pt) REVERT: C 314 GLN cc_start: 0.8374 (tt0) cc_final: 0.8063 (tt0) REVERT: C 318 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.6783 (p90) REVERT: C 660 TYR cc_start: 0.8510 (m-80) cc_final: 0.8075 (m-80) REVERT: C 661 GLU cc_start: 0.7550 (mt-10) cc_final: 0.6626 (mm-30) REVERT: C 790 LYS cc_start: 0.8273 (mtpp) cc_final: 0.7938 (mtpp) REVERT: C 811 LYS cc_start: 0.6109 (mtmt) cc_final: 0.5675 (ptpt) REVERT: C 823 PHE cc_start: 0.7937 (m-80) cc_final: 0.7707 (m-80) REVERT: C 868 GLU cc_start: 0.6180 (mm-30) cc_final: 0.5575 (mp0) REVERT: C 875 SER cc_start: 0.8110 (t) cc_final: 0.7750 (p) REVERT: C 886 TRP cc_start: 0.7272 (p90) cc_final: 0.6525 (p90) REVERT: C 916 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7157 (tt) REVERT: C 921 LYS cc_start: 0.6625 (mtpp) cc_final: 0.5981 (mmpt) REVERT: C 995 ARG cc_start: 0.6966 (mtp85) cc_final: 0.6737 (mtp85) REVERT: C 1005 GLN cc_start: 0.7569 (tp40) cc_final: 0.7250 (mm-40) REVERT: C 1045 LYS cc_start: 0.7918 (mmmt) cc_final: 0.7558 (tttt) REVERT: D 34 MET cc_start: 0.3566 (OUTLIER) cc_final: 0.3259 (mmm) REVERT: D 67 ARG cc_start: 0.2010 (ptp-170) cc_final: 0.1734 (mtt180) REVERT: D 324 PHE cc_start: 0.1490 (m-80) cc_final: 0.0488 (t80) REVERT: E 190 GLN cc_start: 0.5896 (OUTLIER) cc_final: 0.4845 (mp10) REVERT: E 230 TYR cc_start: 0.3028 (p90) cc_final: 0.2507 (p90) REVERT: F 34 MET cc_start: 0.3877 (mmp) cc_final: 0.3361 (mmm) REVERT: F 153 ARG cc_start: 0.4363 (ttp80) cc_final: 0.3227 (mmt90) REVERT: F 277 GLN cc_start: 0.1133 (OUTLIER) cc_final: 0.0646 (tp40) REVERT: F 451 GLU cc_start: 0.2216 (mp0) cc_final: 0.1341 (mt-10) REVERT: G 122 LEU cc_start: 0.1973 (OUTLIER) cc_final: 0.1755 (tt) REVERT: G 124 THR cc_start: 0.0487 (p) cc_final: -0.0081 (t) REVERT: G 192 LEU cc_start: 0.2858 (OUTLIER) cc_final: 0.2504 (tp) REVERT: H 114 MET cc_start: 0.1510 (tpp) cc_final: 0.1182 (tpp) outliers start: 129 outliers final: 105 residues processed: 400 average time/residue: 0.4762 time to fit residues: 320.6643 Evaluate side-chains 416 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 300 time to evaluate : 4.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 349 TYR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 432 SER Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 293 optimal weight: 4.9990 chunk 472 optimal weight: 6.9990 chunk 288 optimal weight: 0.7980 chunk 224 optimal weight: 0.4980 chunk 328 optimal weight: 8.9990 chunk 496 optimal weight: 20.0000 chunk 456 optimal weight: 20.0000 chunk 395 optimal weight: 40.0000 chunk 41 optimal weight: 10.0000 chunk 305 optimal weight: 0.8980 chunk 242 optimal weight: 20.0000 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN F 422 ASN G 13 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4442 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 40039 Z= 0.495 Angle : 0.666 13.515 54488 Z= 0.336 Chirality : 0.049 0.461 6241 Planarity : 0.005 0.088 7004 Dihedral : 5.718 58.935 6063 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.30 % Allowed : 17.77 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.12), residues: 4938 helix: -0.07 (0.18), residues: 749 sheet: -0.28 (0.14), residues: 1385 loop : -1.08 (0.12), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP E 36 HIS 0.005 0.001 HIS C1048 PHE 0.028 0.002 PHE D 29 TYR 0.032 0.002 TYR D 298 ARG 0.014 0.001 ARG F 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 288 time to evaluate : 4.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.6979 (m-40) cc_final: 0.6330 (p0) REVERT: A 239 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6428 (tm-30) REVERT: A 314 GLN cc_start: 0.8112 (tt0) cc_final: 0.7784 (tp40) REVERT: A 319 ARG cc_start: 0.7486 (ptp90) cc_final: 0.6317 (ptm160) REVERT: A 541 PHE cc_start: 0.7339 (p90) cc_final: 0.6859 (p90) REVERT: A 554 GLU cc_start: 0.8554 (pt0) cc_final: 0.7954 (mt-10) REVERT: A 584 ILE cc_start: 0.8281 (mm) cc_final: 0.7769 (mm) REVERT: A 756 TYR cc_start: 0.6476 (OUTLIER) cc_final: 0.6182 (t80) REVERT: A 787 GLN cc_start: 0.8164 (mt0) cc_final: 0.7548 (mt0) REVERT: A 886 TRP cc_start: 0.6934 (p90) cc_final: 0.6467 (p90) REVERT: A 921 LYS cc_start: 0.6886 (mtpp) cc_final: 0.6589 (tttp) REVERT: A 995 ARG cc_start: 0.6619 (tpp80) cc_final: 0.6231 (mtt180) REVERT: A 1017 GLU cc_start: 0.7167 (tt0) cc_final: 0.6881 (tt0) REVERT: A 1045 LYS cc_start: 0.7786 (mmmt) cc_final: 0.7350 (tmtt) REVERT: B 104 TRP cc_start: 0.6165 (m-90) cc_final: 0.5620 (m-90) REVERT: B 271 GLN cc_start: 0.7598 (mt0) cc_final: 0.7078 (mt0) REVERT: B 675 GLN cc_start: 0.6914 (mt0) cc_final: 0.6185 (mt0) REVERT: B 790 LYS cc_start: 0.8529 (mtpp) cc_final: 0.8140 (mtpp) REVERT: B 868 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6388 (mp0) REVERT: B 964 LYS cc_start: 0.7398 (mmtp) cc_final: 0.6842 (mtpp) REVERT: B 985 ASP cc_start: 0.6619 (OUTLIER) cc_final: 0.6257 (p0) REVERT: B 1017 GLU cc_start: 0.6728 (tp30) cc_final: 0.5950 (tt0) REVERT: B 1101 HIS cc_start: 0.7905 (m170) cc_final: 0.7539 (m-70) REVERT: C 104 TRP cc_start: 0.6627 (m-90) cc_final: 0.6209 (m-90) REVERT: C 117 LEU cc_start: 0.5742 (mp) cc_final: 0.5395 (tp) REVERT: C 190 ARG cc_start: 0.6613 (mtt90) cc_final: 0.6411 (mtt180) REVERT: C 202 LYS cc_start: 0.7225 (mttm) cc_final: 0.7003 (mtmm) REVERT: C 237 ARG cc_start: 0.6330 (mtt180) cc_final: 0.5766 (mtp-110) REVERT: C 293 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6542 (pt) REVERT: C 314 GLN cc_start: 0.8418 (tt0) cc_final: 0.8086 (tt0) REVERT: C 318 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.6734 (p90) REVERT: C 661 GLU cc_start: 0.7665 (mt-10) cc_final: 0.6689 (mm-30) REVERT: C 811 LYS cc_start: 0.6107 (mtmt) cc_final: 0.5418 (ptpt) REVERT: C 868 GLU cc_start: 0.6252 (mm-30) cc_final: 0.5603 (mp0) REVERT: C 875 SER cc_start: 0.8136 (t) cc_final: 0.7753 (p) REVERT: C 1005 GLN cc_start: 0.7590 (tp40) cc_final: 0.7230 (mm-40) REVERT: C 1045 LYS cc_start: 0.8020 (mmmt) cc_final: 0.7623 (tttt) REVERT: D 34 MET cc_start: 0.3714 (OUTLIER) cc_final: 0.3221 (mmm) REVERT: D 67 ARG cc_start: 0.2104 (ptp-170) cc_final: 0.1856 (mtt180) REVERT: D 324 PHE cc_start: 0.1582 (m-80) cc_final: 0.0604 (t80) REVERT: E 190 GLN cc_start: 0.6102 (OUTLIER) cc_final: 0.5071 (mp10) REVERT: E 230 TYR cc_start: 0.2998 (p90) cc_final: 0.2472 (p90) REVERT: F 34 MET cc_start: 0.3940 (mmp) cc_final: 0.3567 (mmm) REVERT: F 153 ARG cc_start: 0.4457 (ttp80) cc_final: 0.3278 (mmt90) REVERT: F 451 GLU cc_start: 0.1880 (mp0) cc_final: 0.1026 (mt-10) REVERT: G 124 THR cc_start: 0.0541 (p) cc_final: -0.0059 (t) REVERT: G 192 LEU cc_start: 0.2913 (OUTLIER) cc_final: 0.2553 (tp) REVERT: H 114 MET cc_start: 0.1774 (tpp) cc_final: 0.1471 (tpp) outliers start: 143 outliers final: 121 residues processed: 394 average time/residue: 0.4810 time to fit residues: 322.7791 Evaluate side-chains 410 residues out of total 4332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 281 time to evaluate : 4.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 349 TYR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 432 SER Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 313 optimal weight: 20.0000 chunk 420 optimal weight: 20.0000 chunk 121 optimal weight: 0.8980 chunk 364 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 395 optimal weight: 30.0000 chunk 165 optimal weight: 0.6980 chunk 406 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.265514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.224934 restraints weight = 43936.854| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 2.21 r_work: 0.4194 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4100 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.213 40039 Z= 0.421 Angle : 0.764 59.200 54488 Z= 0.410 Chirality : 0.047 0.516 6241 Planarity : 0.005 0.156 7004 Dihedral : 5.721 58.744 6063 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.12 % Allowed : 17.98 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.12), residues: 4938 helix: -0.04 (0.18), residues: 749 sheet: -0.29 (0.14), residues: 1385 loop : -1.08 (0.12), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP E 36 HIS 0.004 0.001 HIS C 207 PHE 0.024 0.002 PHE D 29 TYR 0.025 0.002 TYR D 298 ARG 0.010 0.000 ARG F 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8554.67 seconds wall clock time: 158 minutes 37.21 seconds (9517.21 seconds total)