Starting phenix.real_space_refine on Wed Jul 24 22:11:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz5_26879/07_2024/7uz5_26879.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz5_26879/07_2024/7uz5_26879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz5_26879/07_2024/7uz5_26879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz5_26879/07_2024/7uz5_26879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz5_26879/07_2024/7uz5_26879.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz5_26879/07_2024/7uz5_26879.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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 120 5.16 5 C 17209 2.51 5 N 4433 2.21 5 O 5289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "H TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 27051 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8204 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1001} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 8204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8204 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1001} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 8204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8204 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1001} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 15.08, per 1000 atoms: 0.56 Number of scatterers: 27051 At special positions: 0 Unit cell: (160.576, 170.56, 197.184, 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 120 16.00 O 5289 8.00 N 4433 7.00 C 17209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " 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 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1312 " - " ASN A 717 " " NAG A1313 " - " ASN A 801 " " NAG A1314 " - " ASN A1074 " " NAG A1315 " - " ASN A1098 " " NAG A1316 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1312 " - " ASN B 717 " " NAG B1313 " - " ASN B 801 " " NAG B1314 " - " ASN B1074 " " NAG B1315 " - " ASN B1098 " " NAG B1316 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 657 " " NAG C1311 " - " ASN C 709 " " NAG C1312 " - " ASN C 717 " " NAG C1313 " - " ASN C 801 " " NAG C1314 " - " ASN C1074 " " NAG C1315 " - " ASN C1098 " " NAG C1316 " - " ASN C1134 " Time building additional restraints: 10.44 Conformation dependent library (CDL) restraints added in 4.6 seconds 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6346 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 62 sheets defined 23.8% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 344 removed outlier: 4.318A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.521A pdb=" N LEU A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 4.009A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.949A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.695A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.949A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.616A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (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 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.645A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.645A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.510A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1147' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.639A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.687A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.637A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.832A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.552A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.503A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.552A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.715A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.671A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (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 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.557A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.814A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.714A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1141 through 1147' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.832A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.513A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.889A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.649A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (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 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: 3.722A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.507A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1147 removed outlier: 4.204A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1142 through 1147' Processing helix chain 'H' and resid 69 through 72 removed outlier: 3.522A pdb=" N LYS H 72 " --> pdb=" O GLN H 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 69 through 72' Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'L' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 8.387A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.990A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 70 Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 164 removed outlier: 4.365A pdb=" N TRP A 152 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR A 144 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU A 154 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY A 142 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLU A 156 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE A 140 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 13.947A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 13.541A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.578A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.329A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.639A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.558A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.666A pdb=" N LYS C 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.631A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.631A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.671A pdb=" N LYS A 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC1, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 29 through 30 removed outlier: 8.607A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.077A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AC6, first strand: chain 'B' and resid 151 through 172 removed outlier: 4.762A pdb=" N TRP B 152 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR B 144 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 13.122A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.994A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 13.041A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.728A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.167A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.748A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.813A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.639A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.904A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.128A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AE2, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AE3, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.722A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.934A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.668A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.315A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.497A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 12.410A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.690A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 13.187A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 13.338A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 11.389A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.899A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 11.315A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.497A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 12.410A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.188A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 324 through 327 removed outlier: 7.507A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.569A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.809A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.545A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.716A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF8, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG1, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AG2, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AG3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AG4, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.607A pdb=" N MET H 39 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.560A pdb=" N TYR H 117 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.739A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.520A pdb=" N GLN L 106 " --> pdb=" O THR L 117 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR L 117 " --> pdb=" O GLN L 106 " (cutoff:3.500A) 1058 hydrogen bonds defined for protein. 2883 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: 12.48 Time building geometry restraints manager: 11.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8594 1.34 - 1.46: 6037 1.46 - 1.58: 12894 1.58 - 1.70: 0 1.70 - 1.82: 155 Bond restraints: 27680 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CA GLN C 913 " pdb=" C GLN C 913 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.38e-02 5.25e+03 6.49e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" CA GLN A 913 " pdb=" C GLN A 913 " ideal model delta sigma weight residual 1.522 1.490 0.033 1.38e-02 5.25e+03 5.56e+00 bond pdb=" CA GLN B 913 " pdb=" C GLN B 913 " ideal model delta sigma weight residual 1.522 1.490 0.032 1.38e-02 5.25e+03 5.43e+00 ... (remaining 27675 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.06: 514 105.06 - 112.32: 14285 112.32 - 119.58: 8472 119.58 - 126.84: 14129 126.84 - 134.10: 307 Bond angle restraints: 37707 Sorted by residual: angle pdb=" N ASN A1074 " pdb=" CA ASN A1074 " pdb=" C ASN A1074 " ideal model delta sigma weight residual 110.48 104.86 5.62 1.48e+00 4.57e-01 1.44e+01 angle pdb=" C ASN A 121 " pdb=" N ASN A 122 " pdb=" CA ASN A 122 " ideal model delta sigma weight residual 121.86 116.37 5.49 1.65e+00 3.67e-01 1.11e+01 angle pdb=" N ILE A 666 " pdb=" CA ILE A 666 " pdb=" C ILE A 666 " ideal model delta sigma weight residual 111.62 109.02 2.60 7.90e-01 1.60e+00 1.08e+01 angle pdb=" CB ASN A1074 " pdb=" CG ASN A1074 " pdb=" ND2 ASN A1074 " ideal model delta sigma weight residual 116.40 121.28 -4.88 1.50e+00 4.44e-01 1.06e+01 angle pdb=" CA GLN C 173 " pdb=" CB GLN C 173 " pdb=" CG GLN C 173 " ideal model delta sigma weight residual 114.10 120.37 -6.27 2.00e+00 2.50e-01 9.83e+00 ... (remaining 37702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.03: 16223 25.03 - 50.06: 684 50.06 - 75.09: 96 75.09 - 100.11: 33 100.11 - 125.14: 13 Dihedral angle restraints: 17049 sinusoidal: 7166 harmonic: 9883 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -37.71 -48.29 1 1.00e+01 1.00e-02 3.21e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -39.75 -46.25 1 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -40.41 -45.59 1 1.00e+01 1.00e-02 2.88e+01 ... (remaining 17046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4165 0.098 - 0.196: 225 0.196 - 0.294: 5 0.294 - 0.392: 2 0.392 - 0.490: 3 Chirality restraints: 4400 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" C1 NAG B1314 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1314 " pdb=" O5 NAG B1314 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.95e+00 ... (remaining 4397 not shown) Planarity restraints: 4874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.058 5.00e-02 4.00e+02 8.74e-02 1.22e+01 pdb=" N PRO B 987 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1078 " -0.057 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO B1079 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B1079 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B1079 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " -0.023 2.00e-02 2.50e+03 2.15e-02 5.77e+00 pdb=" CG ASN A1074 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " 0.011 2.00e-02 2.50e+03 pdb=" C1 NAG A1314 " -0.019 2.00e-02 2.50e+03 ... (remaining 4871 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 523 2.68 - 3.24: 26134 3.24 - 3.79: 41928 3.79 - 4.35: 56714 4.35 - 4.90: 93737 Nonbonded interactions: 219036 Sorted by model distance: nonbonded pdb=" O GLU B1031 " pdb=" OG SER B1037 " model vdw 2.126 2.440 nonbonded pdb=" O GLY L 36 " pdb=" OH TYR L 87 " model vdw 2.187 2.440 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.196 2.440 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.204 2.440 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.228 2.440 ... (remaining 219031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.330 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 74.750 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.120 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 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 : 0.004 0.066 27680 Z= 0.279 Angle : 0.613 9.027 37707 Z= 0.331 Chirality : 0.047 0.490 4400 Planarity : 0.004 0.087 4826 Dihedral : 14.162 125.142 10589 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.07 % Allowed : 0.69 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: 0.31 (0.14), residues: 3357 helix: 1.45 (0.20), residues: 638 sheet: 0.55 (0.18), residues: 838 loop : -0.35 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 56 HIS 0.010 0.001 HIS A1064 PHE 0.025 0.002 PHE C 906 TYR 0.021 0.001 TYR C 170 ARG 0.005 0.000 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 228 time to evaluate : 3.014 Fit side-chains REVERT: A 65 PHE cc_start: 0.7277 (m-80) cc_final: 0.6872 (m-80) REVERT: A 663 ASP cc_start: 0.8168 (m-30) cc_final: 0.7786 (m-30) REVERT: A 752 LEU cc_start: 0.8852 (tt) cc_final: 0.8626 (tt) REVERT: A 997 ILE cc_start: 0.9000 (mt) cc_final: 0.8792 (mt) REVERT: B 206 LYS cc_start: 0.7980 (tptp) cc_final: 0.7492 (tptp) REVERT: B 957 GLN cc_start: 0.7997 (tm130) cc_final: 0.7488 (tm-30) REVERT: C 140 PHE cc_start: 0.7164 (p90) cc_final: 0.6845 (p90) REVERT: C 160 TYR cc_start: 0.7772 (p90) cc_final: 0.7428 (p90) REVERT: C 529 LYS cc_start: 0.6964 (tmtt) cc_final: 0.6744 (tmtt) REVERT: C 974 SER cc_start: 0.9130 (t) cc_final: 0.8897 (t) REVERT: H 14 MET cc_start: 0.6561 (ttt) cc_final: 0.5476 (pmm) outliers start: 2 outliers final: 0 residues processed: 229 average time/residue: 0.3383 time to fit residues: 131.6824 Evaluate side-chains 168 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 0.9990 chunk 255 optimal weight: 50.0000 chunk 141 optimal weight: 50.0000 chunk 87 optimal weight: 0.9990 chunk 172 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 chunk 264 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 196 optimal weight: 0.7980 chunk 306 optimal weight: 0.0030 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 370 ASN A 804 GLN A 935 GLN A1036 GLN A1054 GLN A1142 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 965 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27680 Z= 0.169 Angle : 0.552 10.964 37707 Z= 0.277 Chirality : 0.047 0.416 4400 Planarity : 0.004 0.063 4826 Dihedral : 9.126 107.620 4653 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.86 % Allowed : 6.10 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: 0.49 (0.14), residues: 3357 helix: 1.83 (0.20), residues: 649 sheet: 0.65 (0.18), residues: 806 loop : -0.33 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 104 HIS 0.005 0.001 HIS C1064 PHE 0.021 0.001 PHE B 168 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 200 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7313 (m-80) cc_final: 0.7036 (m-80) REVERT: A 92 PHE cc_start: 0.5948 (t80) cc_final: 0.5744 (t80) REVERT: A 584 ILE cc_start: 0.8896 (mm) cc_final: 0.8588 (mp) REVERT: A 663 ASP cc_start: 0.8154 (m-30) cc_final: 0.7808 (m-30) REVERT: A 752 LEU cc_start: 0.8839 (tt) cc_final: 0.8566 (tt) REVERT: A 950 ASP cc_start: 0.7767 (t0) cc_final: 0.7490 (t0) REVERT: B 168 PHE cc_start: 0.8663 (t80) cc_final: 0.8170 (t80) REVERT: B 931 ILE cc_start: 0.7119 (mm) cc_final: 0.6879 (tp) REVERT: B 957 GLN cc_start: 0.7962 (tm130) cc_final: 0.7413 (tm-30) REVERT: B 979 ASP cc_start: 0.7437 (t70) cc_final: 0.7140 (t0) REVERT: B 994 ASP cc_start: 0.8508 (t0) cc_final: 0.8203 (t70) REVERT: C 140 PHE cc_start: 0.7275 (p90) cc_final: 0.7073 (p90) REVERT: C 160 TYR cc_start: 0.7864 (p90) cc_final: 0.7506 (p90) REVERT: C 536 ASN cc_start: 0.8305 (m-40) cc_final: 0.7957 (m-40) REVERT: C 562 PHE cc_start: 0.6311 (t80) cc_final: 0.6060 (t80) REVERT: C 895 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: C 974 SER cc_start: 0.8985 (t) cc_final: 0.8729 (t) REVERT: H 103 PHE cc_start: 0.5084 (m-80) cc_final: 0.4828 (m-80) outliers start: 25 outliers final: 17 residues processed: 213 average time/residue: 0.3249 time to fit residues: 119.8471 Evaluate side-chains 186 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 170 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 254 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 306 optimal weight: 2.9990 chunk 331 optimal weight: 50.0000 chunk 273 optimal weight: 5.9990 chunk 304 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 245 optimal weight: 50.0000 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 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 953 ASN A 955 ASN B 481 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 914 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 957 GLN C 146 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27680 Z= 0.250 Angle : 0.549 10.290 37707 Z= 0.274 Chirality : 0.047 0.416 4400 Planarity : 0.004 0.058 4826 Dihedral : 7.725 100.517 4653 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.27 % Allowed : 8.64 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: 0.47 (0.14), residues: 3357 helix: 1.90 (0.20), residues: 647 sheet: 0.53 (0.18), residues: 823 loop : -0.32 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 56 HIS 0.005 0.001 HIS B1064 PHE 0.021 0.002 PHE C 782 TYR 0.022 0.001 TYR A1067 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 181 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7395 (m-80) cc_final: 0.7152 (m-80) REVERT: A 92 PHE cc_start: 0.5971 (t80) cc_final: 0.5750 (t80) REVERT: A 584 ILE cc_start: 0.8868 (mm) cc_final: 0.8557 (mp) REVERT: A 663 ASP cc_start: 0.8228 (m-30) cc_final: 0.7901 (m-30) REVERT: A 752 LEU cc_start: 0.8803 (tt) cc_final: 0.8500 (tt) REVERT: B 239 GLN cc_start: 0.5416 (mm-40) cc_final: 0.4831 (mm-40) REVERT: B 957 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7475 (tm-30) REVERT: B 979 ASP cc_start: 0.7610 (t70) cc_final: 0.7238 (t0) REVERT: B 994 ASP cc_start: 0.8528 (t0) cc_final: 0.8235 (t70) REVERT: C 140 PHE cc_start: 0.7339 (p90) cc_final: 0.7028 (p90) REVERT: C 160 TYR cc_start: 0.7880 (p90) cc_final: 0.7536 (p90) REVERT: C 536 ASN cc_start: 0.8352 (m-40) cc_final: 0.8015 (m-40) REVERT: C 895 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: H 103 PHE cc_start: 0.5200 (m-80) cc_final: 0.4950 (m-80) REVERT: L 11 MET cc_start: 0.3003 (ppp) cc_final: 0.2590 (ppp) outliers start: 37 outliers final: 27 residues processed: 202 average time/residue: 0.3268 time to fit residues: 114.4740 Evaluate side-chains 188 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 302 optimal weight: 1.9990 chunk 230 optimal weight: 20.0000 chunk 159 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 146 optimal weight: 50.0000 chunk 205 optimal weight: 0.9990 chunk 307 optimal weight: 2.9990 chunk 325 optimal weight: 50.0000 chunk 160 optimal weight: 0.0980 chunk 291 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27680 Z= 0.250 Angle : 0.550 9.749 37707 Z= 0.272 Chirality : 0.048 0.415 4400 Planarity : 0.004 0.054 4826 Dihedral : 7.151 89.129 4653 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.99 % Allowed : 9.60 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: 0.43 (0.14), residues: 3357 helix: 1.91 (0.20), residues: 647 sheet: 0.43 (0.18), residues: 822 loop : -0.31 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP L 56 HIS 0.005 0.001 HIS A1064 PHE 0.023 0.002 PHE C 782 TYR 0.022 0.001 TYR A1067 ARG 0.009 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 181 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7447 (m-80) cc_final: 0.7206 (m-80) REVERT: A 584 ILE cc_start: 0.8847 (mm) cc_final: 0.8546 (mp) REVERT: A 663 ASP cc_start: 0.8260 (m-30) cc_final: 0.7908 (m-30) REVERT: B 168 PHE cc_start: 0.8569 (t80) cc_final: 0.8022 (t80) REVERT: B 239 GLN cc_start: 0.5531 (mm-40) cc_final: 0.4897 (mm-40) REVERT: B 957 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7565 (tm-30) REVERT: B 979 ASP cc_start: 0.7810 (t70) cc_final: 0.7419 (t0) REVERT: B 994 ASP cc_start: 0.8600 (t0) cc_final: 0.8319 (t0) REVERT: C 140 PHE cc_start: 0.7404 (p90) cc_final: 0.7078 (p90) REVERT: C 160 TYR cc_start: 0.7907 (p90) cc_final: 0.7552 (p90) REVERT: C 536 ASN cc_start: 0.8375 (m-40) cc_final: 0.8052 (m-40) REVERT: C 895 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: C 979 ASP cc_start: 0.8332 (t0) cc_final: 0.8112 (t0) REVERT: H 103 PHE cc_start: 0.5276 (m-80) cc_final: 0.5022 (m-80) REVERT: L 11 MET cc_start: 0.2904 (ppp) cc_final: 0.2541 (ppp) outliers start: 58 outliers final: 38 residues processed: 223 average time/residue: 0.3283 time to fit residues: 126.8035 Evaluate side-chains 204 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain L residue 56 TRP Chi-restraints excluded: chain L residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 271 optimal weight: 0.1980 chunk 184 optimal weight: 0.7980 chunk 4 optimal weight: 30.0000 chunk 242 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 277 optimal weight: 0.8980 chunk 225 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 292 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27680 Z= 0.181 Angle : 0.524 9.690 37707 Z= 0.258 Chirality : 0.046 0.421 4400 Planarity : 0.003 0.052 4826 Dihedral : 6.777 73.455 4653 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.61 % Allowed : 10.91 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: 0.45 (0.14), residues: 3357 helix: 1.96 (0.20), residues: 654 sheet: 0.40 (0.18), residues: 814 loop : -0.31 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP L 56 HIS 0.004 0.001 HIS B1083 PHE 0.017 0.001 PHE A1121 TYR 0.020 0.001 TYR C 170 ARG 0.003 0.000 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 184 time to evaluate : 3.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7445 (m-80) cc_final: 0.7044 (m-10) REVERT: A 584 ILE cc_start: 0.8867 (mm) cc_final: 0.8581 (mp) REVERT: A 663 ASP cc_start: 0.8230 (m-30) cc_final: 0.7908 (m-30) REVERT: B 104 TRP cc_start: 0.6393 (m-90) cc_final: 0.5950 (m-90) REVERT: B 239 GLN cc_start: 0.5517 (OUTLIER) cc_final: 0.4944 (mm-40) REVERT: B 957 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7481 (tm-30) REVERT: B 979 ASP cc_start: 0.7857 (t70) cc_final: 0.7460 (t0) REVERT: B 994 ASP cc_start: 0.8595 (t0) cc_final: 0.8328 (t0) REVERT: B 1029 MET cc_start: 0.7805 (tpp) cc_final: 0.7554 (ttm) REVERT: C 140 PHE cc_start: 0.7243 (p90) cc_final: 0.6880 (p90) REVERT: C 160 TYR cc_start: 0.7893 (p90) cc_final: 0.7526 (p90) REVERT: C 529 LYS cc_start: 0.6812 (tmtt) cc_final: 0.6399 (tmtt) REVERT: C 536 ASN cc_start: 0.8342 (m-40) cc_final: 0.7938 (m110) REVERT: H 55 GLU cc_start: 0.8138 (pt0) cc_final: 0.7824 (pp20) REVERT: H 103 PHE cc_start: 0.5373 (m-80) cc_final: 0.5083 (m-80) REVERT: L 11 MET cc_start: 0.2880 (ppp) cc_final: 0.2556 (ppp) outliers start: 47 outliers final: 32 residues processed: 215 average time/residue: 0.3214 time to fit residues: 120.6553 Evaluate side-chains 195 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 162 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain L residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 109 optimal weight: 0.0170 chunk 293 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 191 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 326 optimal weight: 20.0000 chunk 270 optimal weight: 10.0000 chunk 150 optimal weight: 30.0000 chunk 27 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 804 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 856 ASN B 914 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C 965 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27680 Z= 0.158 Angle : 0.515 9.598 37707 Z= 0.254 Chirality : 0.046 0.414 4400 Planarity : 0.003 0.051 4826 Dihedral : 6.408 66.869 4653 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.82 % Allowed : 11.52 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: 0.46 (0.14), residues: 3357 helix: 1.97 (0.20), residues: 661 sheet: 0.39 (0.17), residues: 834 loop : -0.30 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP L 56 HIS 0.005 0.001 HIS A1048 PHE 0.026 0.001 PHE B 168 TYR 0.018 0.001 TYR A 170 ARG 0.007 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 174 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7469 (m-80) cc_final: 0.7037 (m-10) REVERT: A 584 ILE cc_start: 0.8887 (mm) cc_final: 0.8590 (mp) REVERT: A 663 ASP cc_start: 0.8222 (m-30) cc_final: 0.7913 (m-30) REVERT: B 239 GLN cc_start: 0.5489 (OUTLIER) cc_final: 0.4860 (mm-40) REVERT: B 650 LEU cc_start: 0.7722 (pp) cc_final: 0.7503 (pp) REVERT: B 957 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 979 ASP cc_start: 0.7861 (t70) cc_final: 0.7493 (t0) REVERT: B 994 ASP cc_start: 0.8524 (t0) cc_final: 0.8269 (t0) REVERT: B 1029 MET cc_start: 0.7813 (tpp) cc_final: 0.7492 (ttm) REVERT: C 84 LEU cc_start: 0.6843 (mt) cc_final: 0.6610 (mp) REVERT: C 140 PHE cc_start: 0.7272 (p90) cc_final: 0.6974 (p90) REVERT: C 160 TYR cc_start: 0.7889 (p90) cc_final: 0.7522 (p90) REVERT: C 529 LYS cc_start: 0.6823 (tmtt) cc_final: 0.6400 (tmtt) REVERT: C 536 ASN cc_start: 0.8325 (m-40) cc_final: 0.7915 (m110) REVERT: C 950 ASP cc_start: 0.7863 (m-30) cc_final: 0.7523 (m-30) REVERT: H 55 GLU cc_start: 0.8176 (pt0) cc_final: 0.7921 (pp20) REVERT: H 103 PHE cc_start: 0.5426 (m-80) cc_final: 0.5147 (m-80) REVERT: L 11 MET cc_start: 0.2734 (ppp) cc_final: 0.2484 (ppp) outliers start: 53 outliers final: 37 residues processed: 211 average time/residue: 0.3288 time to fit residues: 121.3419 Evaluate side-chains 201 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain L residue 56 TRP Chi-restraints excluded: chain L residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 314 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 185 optimal weight: 0.5980 chunk 238 optimal weight: 4.9990 chunk 184 optimal weight: 0.6980 chunk 274 optimal weight: 0.8980 chunk 182 optimal weight: 0.0970 chunk 324 optimal weight: 50.0000 chunk 203 optimal weight: 0.9990 chunk 198 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27680 Z= 0.150 Angle : 0.507 9.592 37707 Z= 0.250 Chirality : 0.046 0.414 4400 Planarity : 0.003 0.051 4826 Dihedral : 6.145 59.467 4653 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.65 % Allowed : 12.00 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: 0.53 (0.14), residues: 3357 helix: 2.07 (0.21), residues: 656 sheet: 0.45 (0.17), residues: 833 loop : -0.27 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP L 56 HIS 0.005 0.001 HIS C1064 PHE 0.017 0.001 PHE A 92 TYR 0.021 0.001 TYR C 170 ARG 0.002 0.000 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 175 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7494 (m-80) cc_final: 0.7027 (m-10) REVERT: A 584 ILE cc_start: 0.8873 (mm) cc_final: 0.8671 (mp) REVERT: A 663 ASP cc_start: 0.8255 (m-30) cc_final: 0.7919 (m-30) REVERT: B 239 GLN cc_start: 0.5463 (OUTLIER) cc_final: 0.4829 (mm-40) REVERT: B 650 LEU cc_start: 0.7683 (pp) cc_final: 0.7442 (pp) REVERT: B 957 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7473 (tm-30) REVERT: B 979 ASP cc_start: 0.7887 (t70) cc_final: 0.7519 (t0) REVERT: B 994 ASP cc_start: 0.8497 (t0) cc_final: 0.8259 (t0) REVERT: B 1002 GLN cc_start: 0.8259 (tp40) cc_final: 0.8017 (tp-100) REVERT: B 1029 MET cc_start: 0.7762 (tpp) cc_final: 0.7502 (ttm) REVERT: C 65 PHE cc_start: 0.8014 (m-80) cc_final: 0.7776 (m-80) REVERT: C 84 LEU cc_start: 0.6859 (mt) cc_final: 0.6637 (mp) REVERT: C 140 PHE cc_start: 0.7280 (p90) cc_final: 0.6979 (p90) REVERT: C 160 TYR cc_start: 0.7876 (p90) cc_final: 0.7511 (p90) REVERT: C 529 LYS cc_start: 0.6819 (tmtt) cc_final: 0.6330 (tmtt) REVERT: C 752 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8827 (tt) REVERT: C 950 ASP cc_start: 0.7852 (m-30) cc_final: 0.7521 (m-30) REVERT: H 89 MET cc_start: -0.1816 (tpp) cc_final: -0.2208 (tpp) REVERT: H 103 PHE cc_start: 0.5380 (m-80) cc_final: 0.5078 (m-80) REVERT: L 11 MET cc_start: 0.2820 (ppp) cc_final: 0.2547 (ppp) outliers start: 48 outliers final: 40 residues processed: 208 average time/residue: 0.3311 time to fit residues: 121.7491 Evaluate side-chains 209 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 167 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain L residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 200 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 193 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 160 optimal weight: 0.4980 chunk 30 optimal weight: 7.9990 chunk 255 optimal weight: 30.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 856 ASN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 HIS ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 27680 Z= 0.353 Angle : 0.598 11.808 37707 Z= 0.297 Chirality : 0.048 0.395 4400 Planarity : 0.004 0.051 4826 Dihedral : 6.322 58.903 4653 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.13 % Allowed : 11.63 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: 0.31 (0.14), residues: 3357 helix: 1.72 (0.20), residues: 648 sheet: 0.29 (0.17), residues: 845 loop : -0.34 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP L 56 HIS 0.006 0.001 HIS C1064 PHE 0.023 0.002 PHE B 168 TYR 0.029 0.001 TYR A1067 ARG 0.017 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 166 time to evaluate : 3.180 Fit side-chains revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7476 (m-80) cc_final: 0.7239 (m-80) REVERT: A 584 ILE cc_start: 0.8852 (mm) cc_final: 0.8556 (mp) REVERT: B 104 TRP cc_start: 0.6437 (m-90) cc_final: 0.6020 (m-90) REVERT: B 239 GLN cc_start: 0.5538 (OUTLIER) cc_final: 0.4964 (mm-40) REVERT: B 904 TYR cc_start: 0.7604 (m-10) cc_final: 0.6988 (m-10) REVERT: B 957 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7669 (tm-30) REVERT: B 979 ASP cc_start: 0.7940 (t70) cc_final: 0.7600 (t0) REVERT: B 994 ASP cc_start: 0.8632 (t0) cc_final: 0.8404 (t0) REVERT: B 1029 MET cc_start: 0.7875 (tpp) cc_final: 0.7438 (ttm) REVERT: C 84 LEU cc_start: 0.7040 (mt) cc_final: 0.6811 (mp) REVERT: C 140 PHE cc_start: 0.7560 (p90) cc_final: 0.7270 (p90) REVERT: C 160 TYR cc_start: 0.7945 (p90) cc_final: 0.7571 (p90) REVERT: C 529 LYS cc_start: 0.6763 (tmtt) cc_final: 0.6277 (tmtt) REVERT: C 536 ASN cc_start: 0.8492 (m-40) cc_final: 0.8142 (m-40) REVERT: C 723 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.8077 (p) REVERT: H 55 GLU cc_start: 0.8068 (pt0) cc_final: 0.7790 (pp20) REVERT: H 89 MET cc_start: -0.1659 (tpp) cc_final: -0.2000 (tpp) REVERT: H 103 PHE cc_start: 0.5357 (m-80) cc_final: 0.5028 (m-80) REVERT: L 11 MET cc_start: 0.2778 (ppp) cc_final: 0.2450 (ppp) outliers start: 62 outliers final: 43 residues processed: 212 average time/residue: 0.3381 time to fit residues: 125.9832 Evaluate side-chains 203 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 158 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 96 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 295 optimal weight: 0.9980 chunk 311 optimal weight: 1.9990 chunk 283 optimal weight: 0.7980 chunk 302 optimal weight: 0.7980 chunk 182 optimal weight: 0.0000 chunk 131 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 273 optimal weight: 0.9990 chunk 286 optimal weight: 0.8980 chunk 301 optimal weight: 0.9980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 762 GLN B 856 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27680 Z= 0.163 Angle : 0.521 10.401 37707 Z= 0.257 Chirality : 0.047 0.484 4400 Planarity : 0.003 0.050 4826 Dihedral : 6.069 59.283 4653 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.37 % Allowed : 12.59 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: 0.42 (0.14), residues: 3357 helix: 1.91 (0.20), residues: 657 sheet: 0.32 (0.17), residues: 840 loop : -0.30 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP L 56 HIS 0.006 0.001 HIS A1048 PHE 0.019 0.001 PHE A 92 TYR 0.023 0.001 TYR C 170 ARG 0.002 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 167 time to evaluate : 2.839 Fit side-chains revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7493 (m-80) cc_final: 0.7253 (m-80) REVERT: A 663 ASP cc_start: 0.8221 (m-30) cc_final: 0.7885 (m-30) REVERT: B 168 PHE cc_start: 0.8416 (t80) cc_final: 0.7929 (t80) REVERT: B 239 GLN cc_start: 0.5468 (OUTLIER) cc_final: 0.4857 (mm-40) REVERT: B 957 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7536 (tm-30) REVERT: B 979 ASP cc_start: 0.7955 (t70) cc_final: 0.7620 (t0) REVERT: B 994 ASP cc_start: 0.8576 (t0) cc_final: 0.8330 (t0) REVERT: B 1029 MET cc_start: 0.7823 (tpp) cc_final: 0.7504 (ttm) REVERT: C 84 LEU cc_start: 0.6982 (mt) cc_final: 0.6744 (mp) REVERT: C 160 TYR cc_start: 0.7872 (p90) cc_final: 0.7518 (p90) REVERT: C 529 LYS cc_start: 0.6829 (tmtt) cc_final: 0.6280 (tmtt) REVERT: C 536 ASN cc_start: 0.8341 (m-40) cc_final: 0.7981 (m-40) REVERT: H 55 GLU cc_start: 0.8009 (pt0) cc_final: 0.7371 (pm20) REVERT: H 89 MET cc_start: -0.1734 (tpp) cc_final: -0.2069 (tpp) REVERT: H 103 PHE cc_start: 0.5367 (m-80) cc_final: 0.5043 (m-80) REVERT: L 11 MET cc_start: 0.2723 (ppp) cc_final: 0.2406 (ppp) outliers start: 40 outliers final: 36 residues processed: 194 average time/residue: 0.3123 time to fit residues: 106.4101 Evaluate side-chains 197 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 80 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 198 optimal weight: 2.9990 chunk 320 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 151 optimal weight: 30.0000 chunk 222 optimal weight: 20.0000 chunk 335 optimal weight: 20.0000 chunk 309 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 163 optimal weight: 0.2980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 762 GLN B 856 ASN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 27680 Z= 0.282 Angle : 0.557 10.398 37707 Z= 0.274 Chirality : 0.047 0.393 4400 Planarity : 0.003 0.051 4826 Dihedral : 6.045 58.854 4653 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.47 % Allowed : 12.76 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: 0.36 (0.14), residues: 3357 helix: 1.83 (0.20), residues: 646 sheet: 0.28 (0.18), residues: 843 loop : -0.31 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP L 56 HIS 0.005 0.001 HIS C1064 PHE 0.023 0.001 PHE C 140 TYR 0.024 0.001 TYR A1067 ARG 0.002 0.000 ARG A 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 3.230 Fit side-chains revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7515 (m-80) cc_final: 0.7259 (m-80) REVERT: A 663 ASP cc_start: 0.8299 (m-30) cc_final: 0.7991 (m-30) REVERT: B 104 TRP cc_start: 0.6421 (m-90) cc_final: 0.5993 (m-90) REVERT: B 239 GLN cc_start: 0.5488 (OUTLIER) cc_final: 0.4929 (mm-40) REVERT: B 957 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7616 (tm-30) REVERT: B 979 ASP cc_start: 0.8023 (t70) cc_final: 0.7684 (t0) REVERT: B 994 ASP cc_start: 0.8611 (t0) cc_final: 0.8382 (t0) REVERT: B 1029 MET cc_start: 0.7860 (tpp) cc_final: 0.7421 (ttm) REVERT: C 84 LEU cc_start: 0.7015 (mt) cc_final: 0.6774 (mp) REVERT: C 160 TYR cc_start: 0.7896 (p90) cc_final: 0.7534 (p90) REVERT: C 529 LYS cc_start: 0.6778 (tmtt) cc_final: 0.6288 (tmtt) REVERT: C 536 ASN cc_start: 0.8420 (m-40) cc_final: 0.8048 (m-40) REVERT: H 55 GLU cc_start: 0.7984 (pt0) cc_final: 0.7729 (pp20) REVERT: H 89 MET cc_start: -0.1343 (tpp) cc_final: -0.1638 (tpp) REVERT: H 103 PHE cc_start: 0.5425 (m-80) cc_final: 0.5085 (m-80) REVERT: L 11 MET cc_start: 0.2691 (ppp) cc_final: 0.2352 (ppp) outliers start: 43 outliers final: 40 residues processed: 195 average time/residue: 0.3382 time to fit residues: 115.7335 Evaluate side-chains 201 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 160 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 96 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 212 optimal weight: 3.9990 chunk 284 optimal weight: 0.0010 chunk 81 optimal weight: 0.2980 chunk 246 optimal weight: 50.0000 chunk 39 optimal weight: 30.0000 chunk 74 optimal weight: 0.0970 chunk 267 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 274 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 762 GLN B 856 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.219086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.135601 restraints weight = 42484.883| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 3.78 r_work: 0.3608 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27680 Z= 0.156 Angle : 0.506 9.532 37707 Z= 0.250 Chirality : 0.046 0.400 4400 Planarity : 0.003 0.050 4826 Dihedral : 5.797 58.486 4653 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.37 % Allowed : 12.93 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: 0.47 (0.14), residues: 3357 helix: 1.96 (0.20), residues: 658 sheet: 0.33 (0.17), residues: 837 loop : -0.25 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP L 56 HIS 0.005 0.001 HIS A1048 PHE 0.026 0.001 PHE C 140 TYR 0.022 0.001 TYR C 170 ARG 0.004 0.000 ARG A 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5638.96 seconds wall clock time: 101 minutes 39.72 seconds (6099.72 seconds total)