Starting phenix.real_space_refine on Fri Mar 22 01:38:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csj_26964/03_2024/8csj_26964.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csj_26964/03_2024/8csj_26964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csj_26964/03_2024/8csj_26964.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csj_26964/03_2024/8csj_26964.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csj_26964/03_2024/8csj_26964.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csj_26964/03_2024/8csj_26964.pdb" } resolution = 3.53 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= -0.001 sd= 0.031 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 137 5.16 5 C 20271 2.51 5 N 5269 2.21 5 O 6257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 830": "OD1" <-> "OD2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "D ASP 72": "OD1" <-> "OD2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 32": "OD1" <-> "OD2" Residue "E TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 72": "OD1" <-> "OD2" Residue "F TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 100": "OD1" <-> "OD2" Residue "G ASP 32": "OD1" <-> "OD2" Residue "G GLU 83": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31934 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8740 Classifications: {'peptide': 1120} Link IDs: {'PTRANS': 55, 'TRANS': 1064} Chain breaks: 3 Chain: "H" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 802 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "B" Number of atoms: 8740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8740 Classifications: {'peptide': 1120} Link IDs: {'PTRANS': 55, 'TRANS': 1064} Chain breaks: 3 Chain: "C" Number of atoms: 8583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8583 Classifications: {'peptide': 1099} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1043} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 802 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "F" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "G" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 802 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 16.35, per 1000 atoms: 0.51 Number of scatterers: 31934 At special positions: 0 Unit cell: (173.34, 180.83, 176.55, 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 137 16.00 O 6257 8.00 N 5269 7.00 C 20271 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.04 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 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! Possible link ignored !!! !!! HETATM31398 O3 NAG M 1 69.362 139.196 96.127 1.00250.57 O !!! !!! HETATM31411 N2 NAG M 2 68.449 139.472 95.075 1.00265.55 N !!! !!! N-linked glycan : False !!! !!! O-linked glycan : False !!! !!! Glycan-glycan : True !!! !!! No carbon atom found !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 149 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 74 " " NAG A1311 " - " ASN A 61 " " NAG A1312 " - " ASN A 234 " " NAG A1313 " - " ASN B 234 " " NAG B1201 " - " ASN B 603 " " NAG B1202 " - " ASN B 616 " " NAG B1203 " - " ASN B 657 " " NAG B1204 " - " ASN B 709 " " NAG B1205 " - " ASN B1074 " " NAG B1206 " - " ASN B 149 " " NAG B1207 " - " ASN B 282 " " NAG B1208 " - " ASN B 74 " " NAG B1209 " - " ASN B 61 " " NAG B1210 " - " ASN B 17 " " NAG C1201 " - " ASN C 331 " " NAG C1202 " - " ASN C 343 " " NAG C1203 " - " ASN C 616 " " NAG C1204 " - " ASN C 657 " " NAG C1205 " - " ASN C 709 " " NAG C1206 " - " ASN C1074 " " NAG C1207 " - " ASN C 149 " " NAG C1208 " - " ASN C 74 " " NAG C1209 " - " ASN C 61 " " NAG C1210 " - " ASN C 234 " " NAG J 1 " - " ASN A 17 " " NAG K 1 " - " ASN B 122 " " NAG M 1 " - " ASN C 282 " " NAG N 1 " - " ASN C 122 " " NAG O 1 " - " ASN C 17 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.74 Conformation dependent library (CDL) restraints added in 5.9 seconds 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7476 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 55 sheets defined 20.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.751A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.802A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.616A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 636 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.535A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.639A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.868A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.131A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.122A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) 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: 3.553A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.100A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 4.103A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.624A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.992A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.710A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.623A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 4.082A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.773A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 628 Processing helix chain 'B' and resid 630 through 636 removed outlier: 3.717A pdb=" N ARG B 634 " --> pdb=" O THR B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.626A 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 Processing helix chain 'B' and resid 832 through 840 removed outlier: 3.695A pdb=" N CYS B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.903A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 940 removed outlier: 4.272A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.504A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) 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: 3.724A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.233A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.730A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.717A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.553A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.765A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 940 removed outlier: 4.133A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 6.057A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.977A pdb=" N THR D 87 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.501A pdb=" N ASP E 82 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.512A pdb=" N THR F 87 " --> pdb=" O THR F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.543A pdb=" N ASP G 82 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 27 through 30 current: chain 'A' and resid 77 through 79 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 77 through 79 current: chain 'A' and resid 188 through 197 removed outlier: 3.612A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.601A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 122 removed outlier: 3.947A pdb=" N ASN A 125 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 11.185A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.381A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.545A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.580A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 315 removed outlier: 3.999A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.800A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.532A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.311A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.841A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 711 through 728 current: chain 'A' and resid 1059 through 1077 Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.730A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.817A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.607A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP H 72 " --> pdb=" O THR H 77 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.693A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 77 through 79 current: chain 'B' and resid 188 through 197 removed outlier: 3.766A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.055A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.259A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 154 through 160 removed outlier: 5.632A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.982A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 354 through 358 current: chain 'B' and resid 508 through 516 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.895A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.947A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.545A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.408A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 27 through 30 current: chain 'C' and resid 77 through 79 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 77 through 79 current: chain 'C' and resid 188 through 197 removed outlier: 3.675A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.777A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 222 through 227 current: chain 'C' and resid 285 through 290 Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 85 current: chain 'C' and resid 117 through 121 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 126 through 131 current: chain 'C' and resid 154 through 160 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.234A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.784A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.513A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 551 " --> pdb=" O THR C 588 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE C 584 " --> pdb=" O SER C 555 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.714A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.778A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.467A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.250A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF3, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.620A pdb=" N SER D 70 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.624A pdb=" N GLU D 10 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR D 110 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TRP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 9 through 13 current: chain 'E' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 48 current: chain 'E' and resid 96 through 98 No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'E' and resid 18 through 24 Processing sheet with id=AF7, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.613A pdb=" N SER F 70 " --> pdb=" O TYR F 79 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.543A pdb=" N THR F 110 " --> pdb=" O GLU F 10 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TRP F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N MET F 48 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 9 through 13 current: chain 'G' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 45 through 48 current: chain 'G' and resid 96 through 98 No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'G' and resid 18 through 23 955 hydrogen bonds defined for protein. 2631 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: 15.13 Time building geometry restraints manager: 12.83 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: 10219 1.34 - 1.47: 8178 1.47 - 1.59: 14097 1.59 - 1.71: 2 1.71 - 1.83: 173 Bond restraints: 32669 Sorted by residual: bond pdb=" CA ASP D 100E" pdb=" CB ASP D 100E" ideal model delta sigma weight residual 1.526 1.665 -0.139 1.76e-02 3.23e+03 6.23e+01 bond pdb=" C GLN B 271 " pdb=" O GLN B 271 " ideal model delta sigma weight residual 1.237 1.294 -0.057 1.38e-02 5.25e+03 1.69e+01 bond pdb=" C LEU B 270 " pdb=" N GLN B 271 " ideal model delta sigma weight residual 1.332 1.284 0.048 1.46e-02 4.69e+03 1.07e+01 bond pdb=" CB PRO A 589 " pdb=" CG PRO A 589 " ideal model delta sigma weight residual 1.492 1.640 -0.148 5.00e-02 4.00e+02 8.81e+00 bond pdb=" N GLN C 853 " pdb=" CA GLN C 853 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.74e+00 ... (remaining 32664 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.29: 624 105.29 - 112.58: 16899 112.58 - 119.87: 10880 119.87 - 127.16: 15762 127.16 - 134.45: 309 Bond angle restraints: 44474 Sorted by residual: angle pdb=" CA PRO A 589 " pdb=" N PRO A 589 " pdb=" CD PRO A 589 " ideal model delta sigma weight residual 112.00 99.30 12.70 1.40e+00 5.10e-01 8.23e+01 angle pdb=" O GLN B 271 " pdb=" C GLN B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 121.72 113.74 7.98 9.80e-01 1.04e+00 6.63e+01 angle pdb=" CA GLN B 271 " pdb=" C GLN B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 117.93 127.67 -9.74 1.42e+00 4.96e-01 4.70e+01 angle pdb=" CA LYS E 45 " pdb=" CB LYS E 45 " pdb=" CG LYS E 45 " ideal model delta sigma weight residual 114.10 125.38 -11.28 2.00e+00 2.50e-01 3.18e+01 angle pdb=" CA LEU A 560 " pdb=" CB LEU A 560 " pdb=" CG LEU A 560 " ideal model delta sigma weight residual 116.30 134.45 -18.15 3.50e+00 8.16e-02 2.69e+01 ... (remaining 44469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 17850 18.09 - 36.17: 1572 36.17 - 54.26: 401 54.26 - 72.35: 63 72.35 - 90.44: 54 Dihedral angle restraints: 19940 sinusoidal: 8263 harmonic: 11677 Sorted by residual: dihedral pdb=" CA LEU A 560 " pdb=" C LEU A 560 " pdb=" N PRO A 561 " pdb=" CA PRO A 561 " ideal model delta harmonic sigma weight residual -180.00 -127.71 -52.29 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 -176.56 -90.44 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -175.60 89.60 1 1.00e+01 1.00e-02 9.53e+01 ... (remaining 19937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 5102 0.144 - 0.287: 31 0.287 - 0.431: 1 0.431 - 0.574: 0 0.574 - 0.718: 1 Chirality restraints: 5135 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C1 NAG B1206 " pdb=" ND2 ASN B 149 " pdb=" C2 NAG B1206 " pdb=" O5 NAG B1206 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA PRO A 561 " pdb=" N PRO A 561 " pdb=" C PRO A 561 " pdb=" CB PRO A 561 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 5132 not shown) Planarity restraints: 5741 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 588 " 0.110 5.00e-02 4.00e+02 1.55e-01 3.86e+01 pdb=" N PRO A 589 " -0.268 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 560 " -0.087 5.00e-02 4.00e+02 1.28e-01 2.61e+01 pdb=" N PRO A 561 " 0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 271 " 0.027 2.00e-02 2.50e+03 4.96e-02 2.46e+01 pdb=" C GLN B 271 " -0.086 2.00e-02 2.50e+03 pdb=" O GLN B 271 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO B 272 " 0.030 2.00e-02 2.50e+03 ... (remaining 5738 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 3 2.00 - 2.72: 1514 2.72 - 3.45: 44208 3.45 - 4.17: 76245 4.17 - 4.90: 132176 Nonbonded interactions: 254146 Sorted by model distance: nonbonded pdb=" O ILE C 850 " pdb=" NZ LYS C 854 " model vdw 1.270 2.520 nonbonded pdb=" O3 NAG M 1 " pdb=" N2 NAG M 2 " model vdw 1.420 2.520 nonbonded pdb=" O3 NAG M 1 " pdb=" C2 NAG M 2 " model vdw 1.456 3.470 nonbonded pdb=" OE2 GLU A 298 " pdb=" OG1 THR A 315 " model vdw 2.245 2.440 nonbonded pdb=" OG SER C 349 " pdb=" O LEU C 452 " model vdw 2.253 2.440 ... (remaining 254141 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 828 or (resid 850 and (name N or name CA or nam \ e C or name O or name CB )) or resid 851 through 1147 or resid 1301 through 1310 \ )) selection = (chain 'B' and (resid 14 through 828 or (resid 850 and (name N or name CA or nam \ e C or name O or name CB )) or resid 851 through 1147 or resid 1201 through 1210 \ )) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.110 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 84.190 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.290 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 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 0.148 32669 Z= 0.234 Angle : 0.679 18.145 44474 Z= 0.348 Chirality : 0.048 0.718 5135 Planarity : 0.005 0.155 5703 Dihedral : 14.995 89.862 12332 Min Nonbonded Distance : 1.270 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.20 % Favored : 96.67 % Rotamer: Outliers : 0.29 % Allowed : 16.13 % Favored : 83.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.73 (0.13), residues: 3997 helix: 0.00 (0.18), residues: 661 sheet: 0.56 (0.17), residues: 986 loop : -1.11 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 50 HIS 0.004 0.001 HIS C 625 PHE 0.027 0.001 PHE E 62 TYR 0.033 0.001 TYR H 27 ARG 0.007 0.000 ARG C 634 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 PHE cc_start: 0.8763 (p90) cc_final: 0.8515 (p90) REVERT: A 740 MET cc_start: 0.9218 (tpp) cc_final: 0.8958 (tpp) REVERT: E 37 GLN cc_start: 0.8980 (tp40) cc_final: 0.8349 (tp40) REVERT: F 48 MET cc_start: 0.8753 (pmm) cc_final: 0.8470 (pmm) REVERT: G 95 LEU cc_start: 0.9058 (mp) cc_final: 0.8768 (pp) outliers start: 10 outliers final: 3 residues processed: 140 average time/residue: 0.4092 time to fit residues: 96.4247 Evaluate side-chains 130 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 4.9990 chunk 304 optimal weight: 0.2980 chunk 169 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 315 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 191 optimal weight: 0.7980 chunk 234 optimal weight: 6.9990 chunk 365 optimal weight: 4.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 901 GLN A1011 GLN H 3 GLN B 134 GLN B 317 ASN B 901 GLN C 115 GLN C 134 GLN C 613 GLN C 901 GLN E 37 GLN F 81 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32669 Z= 0.252 Angle : 0.563 13.248 44474 Z= 0.283 Chirality : 0.043 0.464 5135 Planarity : 0.004 0.099 5703 Dihedral : 6.872 58.678 5287 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.65 % Rotamer: Outliers : 1.90 % Allowed : 14.67 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.13), residues: 3997 helix: 1.85 (0.21), residues: 661 sheet: 0.49 (0.16), residues: 1019 loop : -0.90 (0.13), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS L 34 PHE 0.020 0.001 PHE C 562 TYR 0.010 0.001 TYR C1047 ARG 0.003 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 131 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8861 (mp0) REVERT: A 490 PHE cc_start: 0.9519 (t80) cc_final: 0.9311 (t80) REVERT: A 740 MET cc_start: 0.9421 (tpp) cc_final: 0.9091 (tpp) REVERT: B 508 TYR cc_start: 0.9085 (m-80) cc_final: 0.8576 (t80) REVERT: C 22 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8064 (p) REVERT: C 900 MET cc_start: 0.9332 (mmm) cc_final: 0.8725 (mmt) REVERT: E 37 GLN cc_start: 0.8927 (tp-100) cc_final: 0.8688 (tp40) REVERT: G 95 LEU cc_start: 0.9175 (mp) cc_final: 0.8885 (pp) outliers start: 66 outliers final: 40 residues processed: 180 average time/residue: 0.3873 time to fit residues: 119.6757 Evaluate side-chains 161 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 120 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 202 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 303 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 365 optimal weight: 40.0000 chunk 395 optimal weight: 10.0000 chunk 325 optimal weight: 0.8980 chunk 362 optimal weight: 40.0000 chunk 124 optimal weight: 8.9990 chunk 293 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN A1088 HIS ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C1083 HIS ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN E 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 32669 Z= 0.428 Angle : 0.719 12.883 44474 Z= 0.372 Chirality : 0.046 0.413 5135 Planarity : 0.005 0.159 5703 Dihedral : 6.765 59.052 5283 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 3.51 % Allowed : 14.87 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.16 (0.13), residues: 3997 helix: 2.06 (0.21), residues: 648 sheet: 0.13 (0.16), residues: 1028 loop : -0.86 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 47 HIS 0.007 0.002 HIS B 655 PHE 0.040 0.002 PHE C 562 TYR 0.026 0.002 TYR D 79 ARG 0.006 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 126 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8848 (pp30) REVERT: A 52 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8235 (tp40) REVERT: A 490 PHE cc_start: 0.9605 (t80) cc_final: 0.9386 (t80) REVERT: B 80 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7632 (p0) REVERT: C 697 MET cc_start: 0.9088 (mmm) cc_final: 0.8728 (tpt) REVERT: C 759 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8866 (t80) REVERT: D 4 LEU cc_start: 0.6466 (pt) cc_final: 0.6254 (pt) REVERT: D 22 CYS cc_start: 0.8136 (OUTLIER) cc_final: 0.6788 (t) REVERT: E 37 GLN cc_start: 0.9229 (tp-100) cc_final: 0.8979 (tp40) REVERT: G 95 LEU cc_start: 0.9365 (mp) cc_final: 0.9160 (pp) outliers start: 122 outliers final: 79 residues processed: 231 average time/residue: 0.3709 time to fit residues: 147.8654 Evaluate side-chains 195 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 111 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 848 ASP 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 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 54 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 361 optimal weight: 0.7980 chunk 274 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 174 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 367 optimal weight: 10.0000 chunk 388 optimal weight: 3.9990 chunk 191 optimal weight: 0.0040 chunk 347 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN B 901 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32669 Z= 0.222 Angle : 0.535 13.388 44474 Z= 0.274 Chirality : 0.043 0.390 5135 Planarity : 0.004 0.065 5703 Dihedral : 6.401 59.737 5283 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 2.42 % Allowed : 15.90 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.13), residues: 3997 helix: 2.43 (0.21), residues: 655 sheet: 0.22 (0.16), residues: 994 loop : -0.84 (0.13), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.004 0.001 HIS L 34 PHE 0.022 0.001 PHE C 562 TYR 0.025 0.001 TYR A 495 ARG 0.004 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 118 time to evaluate : 3.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8771 (pp30) REVERT: A 820 ASP cc_start: 0.9589 (OUTLIER) cc_final: 0.9191 (m-30) REVERT: H 3 GLN cc_start: 0.9030 (mm110) cc_final: 0.8670 (mm-40) REVERT: B 584 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8608 (tp) REVERT: D 100 PHE cc_start: 0.8401 (m-80) cc_final: 0.7898 (t80) REVERT: F 34 MET cc_start: 0.9297 (mmm) cc_final: 0.8912 (mmm) REVERT: G 95 LEU cc_start: 0.9323 (mp) cc_final: 0.9112 (pp) outliers start: 84 outliers final: 55 residues processed: 191 average time/residue: 0.3925 time to fit residues: 130.0612 Evaluate side-chains 165 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 107 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 323 optimal weight: 0.2980 chunk 220 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 289 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 331 optimal weight: 7.9990 chunk 268 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 348 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 487 ASN A 644 GLN A 955 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 32669 Z= 0.320 Angle : 0.591 14.047 44474 Z= 0.299 Chirality : 0.043 0.387 5135 Planarity : 0.004 0.056 5703 Dihedral : 6.259 59.988 5283 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.40 % Rotamer: Outliers : 2.82 % Allowed : 16.16 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.07 (0.13), residues: 3997 helix: 2.22 (0.21), residues: 676 sheet: 0.11 (0.16), residues: 983 loop : -0.81 (0.13), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 258 HIS 0.005 0.001 HIS C 655 PHE 0.033 0.001 PHE A 490 TYR 0.013 0.001 TYR B 396 ARG 0.004 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 114 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8764 (pp30) REVERT: A 52 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8285 (tp40) REVERT: A 612 TYR cc_start: 0.8863 (m-80) cc_final: 0.8614 (m-10) REVERT: A 820 ASP cc_start: 0.9597 (OUTLIER) cc_final: 0.9203 (m-30) REVERT: H 3 GLN cc_start: 0.9071 (mm110) cc_final: 0.8675 (mm-40) REVERT: B 14 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8693 (pp30) REVERT: B 584 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8528 (tp) REVERT: C 759 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8851 (t80) REVERT: C 1146 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.7943 (m-30) REVERT: D 34 MET cc_start: 0.9183 (tpt) cc_final: 0.8908 (tpt) REVERT: D 100 PHE cc_start: 0.8489 (m-80) cc_final: 0.8058 (t80) outliers start: 98 outliers final: 71 residues processed: 200 average time/residue: 0.4015 time to fit residues: 136.6596 Evaluate side-chains 186 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 108 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1146 ASP Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 130 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 chunk 76 optimal weight: 0.0870 chunk 228 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 388 optimal weight: 20.0000 chunk 322 optimal weight: 0.7980 chunk 180 optimal weight: 20.0000 chunk 32 optimal weight: 0.0980 chunk 128 optimal weight: 5.9990 chunk 204 optimal weight: 0.8980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 536 ASN B 321 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 32669 Z= 0.145 Angle : 0.506 14.166 44474 Z= 0.254 Chirality : 0.043 0.388 5135 Planarity : 0.003 0.054 5703 Dihedral : 6.125 59.784 5283 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.62 % Rotamer: Outliers : 2.50 % Allowed : 16.80 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3997 helix: 2.40 (0.21), residues: 674 sheet: 0.23 (0.16), residues: 992 loop : -0.75 (0.13), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.002 0.000 HIS B 625 PHE 0.022 0.001 PHE A 486 TYR 0.013 0.001 TYR A 369 ARG 0.011 0.000 ARG G 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 109 time to evaluate : 3.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8812 (pp30) REVERT: A 52 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8332 (tp40) REVERT: A 298 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8539 (tm-30) REVERT: A 536 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7374 (p0) REVERT: A 540 ASN cc_start: 0.0237 (OUTLIER) cc_final: -0.0788 (t0) REVERT: A 627 ASP cc_start: 0.9413 (OUTLIER) cc_final: 0.9136 (p0) REVERT: A 697 MET cc_start: 0.9289 (ttm) cc_final: 0.8644 (ttm) REVERT: A 820 ASP cc_start: 0.9561 (OUTLIER) cc_final: 0.9156 (m-30) REVERT: H 3 GLN cc_start: 0.9015 (mm110) cc_final: 0.8610 (mm-40) REVERT: B 434 ILE cc_start: 0.6655 (OUTLIER) cc_final: 0.6452 (mm) REVERT: B 584 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8498 (tp) REVERT: B 697 MET cc_start: 0.9084 (mmm) cc_final: 0.8817 (mmm) REVERT: B 900 MET cc_start: 0.9409 (mmt) cc_final: 0.9112 (mmt) REVERT: B 1083 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.8337 (t-90) REVERT: C 759 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8759 (t80) REVERT: C 1146 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: D 34 MET cc_start: 0.9224 (tpt) cc_final: 0.8849 (tpt) REVERT: D 100 PHE cc_start: 0.8490 (m-80) cc_final: 0.8063 (t80) REVERT: E 37 GLN cc_start: 0.9121 (tp-100) cc_final: 0.8868 (tp40) outliers start: 87 outliers final: 63 residues processed: 189 average time/residue: 0.4110 time to fit residues: 133.3657 Evaluate side-chains 180 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 105 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1146 ASP Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 374 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 221 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 327 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 387 optimal weight: 20.0000 chunk 242 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 32669 Z= 0.410 Angle : 0.646 14.037 44474 Z= 0.326 Chirality : 0.043 0.378 5135 Planarity : 0.004 0.051 5703 Dihedral : 6.254 58.574 5283 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.25 % Favored : 94.70 % Rotamer: Outliers : 3.31 % Allowed : 16.39 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3997 helix: 2.20 (0.21), residues: 678 sheet: 0.00 (0.16), residues: 1029 loop : -0.82 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 258 HIS 0.005 0.001 HIS C 655 PHE 0.040 0.002 PHE A 486 TYR 0.013 0.001 TYR C 170 ARG 0.010 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 107 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8780 (pp30) REVERT: A 52 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8299 (tp40) REVERT: A 540 ASN cc_start: 0.1689 (OUTLIER) cc_final: 0.0802 (t0) REVERT: A 627 ASP cc_start: 0.9424 (OUTLIER) cc_final: 0.9109 (p0) REVERT: A 820 ASP cc_start: 0.9603 (OUTLIER) cc_final: 0.9219 (m-30) REVERT: B 275 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.9125 (m-10) REVERT: B 584 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8566 (tp) REVERT: B 697 MET cc_start: 0.9062 (mmm) cc_final: 0.8821 (mmm) REVERT: B 900 MET cc_start: 0.9449 (mmt) cc_final: 0.9025 (mmt) REVERT: C 759 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8901 (t80) REVERT: C 1146 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: D 100 PHE cc_start: 0.8502 (m-80) cc_final: 0.8079 (t80) REVERT: E 37 GLN cc_start: 0.9206 (tp-100) cc_final: 0.9004 (tp40) REVERT: F 34 MET cc_start: 0.9493 (tpt) cc_final: 0.8984 (tpt) outliers start: 115 outliers final: 87 residues processed: 211 average time/residue: 0.3787 time to fit residues: 139.2142 Evaluate side-chains 199 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 103 time to evaluate : 3.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1146 ASP Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 239 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 263 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 304 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 536 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32669 Z= 0.249 Angle : 0.549 14.945 44474 Z= 0.277 Chirality : 0.043 0.377 5135 Planarity : 0.004 0.048 5703 Dihedral : 6.180 57.866 5283 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 2.70 % Allowed : 17.26 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3997 helix: 2.37 (0.21), residues: 681 sheet: 0.05 (0.16), residues: 1037 loop : -0.76 (0.13), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 47 HIS 0.004 0.001 HIS C 655 PHE 0.042 0.001 PHE A 515 TYR 0.012 0.001 TYR A 369 ARG 0.006 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 112 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8794 (pp30) REVERT: A 52 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8341 (tp40) REVERT: A 536 ASN cc_start: 0.7491 (OUTLIER) cc_final: 0.7103 (p0) REVERT: A 540 ASN cc_start: 0.2000 (OUTLIER) cc_final: 0.1174 (t0) REVERT: A 627 ASP cc_start: 0.9422 (OUTLIER) cc_final: 0.9136 (p0) REVERT: A 697 MET cc_start: 0.9369 (ttm) cc_final: 0.8842 (ttm) REVERT: A 820 ASP cc_start: 0.9575 (OUTLIER) cc_final: 0.9176 (m-30) REVERT: H 3 GLN cc_start: 0.9059 (mm110) cc_final: 0.8622 (mm-40) REVERT: B 275 PHE cc_start: 0.9320 (OUTLIER) cc_final: 0.9103 (m-10) REVERT: B 584 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8407 (tp) REVERT: B 697 MET cc_start: 0.9116 (mmm) cc_final: 0.8872 (mmm) REVERT: B 900 MET cc_start: 0.9423 (mmt) cc_final: 0.8986 (mmt) REVERT: C 697 MET cc_start: 0.8852 (mmm) cc_final: 0.8252 (tpt) REVERT: C 759 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8838 (t80) REVERT: C 1146 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: D 34 MET cc_start: 0.9360 (tpt) cc_final: 0.8638 (tpp) REVERT: D 100 PHE cc_start: 0.8512 (m-80) cc_final: 0.8165 (t80) REVERT: F 34 MET cc_start: 0.9508 (tpt) cc_final: 0.8990 (tpt) outliers start: 94 outliers final: 72 residues processed: 200 average time/residue: 0.4004 time to fit residues: 137.5163 Evaluate side-chains 185 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 103 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1146 ASP Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 352 optimal weight: 1.9990 chunk 371 optimal weight: 10.0000 chunk 338 optimal weight: 5.9990 chunk 361 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 283 optimal weight: 4.9990 chunk 110 optimal weight: 0.0980 chunk 326 optimal weight: 5.9990 chunk 341 optimal weight: 0.6980 chunk 359 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32669 Z= 0.275 Angle : 0.569 14.793 44474 Z= 0.285 Chirality : 0.043 0.377 5135 Planarity : 0.004 0.048 5703 Dihedral : 6.135 58.006 5283 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 2.73 % Allowed : 17.34 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3997 helix: 2.36 (0.21), residues: 681 sheet: 0.09 (0.16), residues: 980 loop : -0.80 (0.13), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 258 HIS 0.004 0.001 HIS C 655 PHE 0.028 0.001 PHE A 515 TYR 0.011 0.001 TYR B 904 ARG 0.006 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 105 time to evaluate : 3.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8810 (pp30) REVERT: A 52 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8309 (tp40) REVERT: A 298 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8476 (tm-30) REVERT: A 540 ASN cc_start: 0.2682 (OUTLIER) cc_final: 0.1831 (t0) REVERT: A 612 TYR cc_start: 0.9065 (m-80) cc_final: 0.8617 (m-80) REVERT: A 627 ASP cc_start: 0.9457 (OUTLIER) cc_final: 0.9175 (p0) REVERT: A 697 MET cc_start: 0.9357 (ttm) cc_final: 0.8785 (ttm) REVERT: A 820 ASP cc_start: 0.9583 (OUTLIER) cc_final: 0.9181 (m-30) REVERT: H 3 GLN cc_start: 0.9072 (mm110) cc_final: 0.8637 (mm-40) REVERT: B 275 PHE cc_start: 0.9323 (OUTLIER) cc_final: 0.9070 (m-10) REVERT: B 584 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8415 (tp) REVERT: B 697 MET cc_start: 0.9094 (mmm) cc_final: 0.8832 (mmm) REVERT: B 900 MET cc_start: 0.9427 (mmt) cc_final: 0.8962 (mmt) REVERT: C 759 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8861 (t80) REVERT: C 1146 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8097 (m-30) REVERT: D 34 MET cc_start: 0.9432 (tpt) cc_final: 0.8695 (tpp) REVERT: D 100 PHE cc_start: 0.8568 (m-80) cc_final: 0.8210 (t80) REVERT: F 18 VAL cc_start: 0.7263 (OUTLIER) cc_final: 0.7058 (p) REVERT: F 34 MET cc_start: 0.9480 (OUTLIER) cc_final: 0.8977 (tpt) outliers start: 95 outliers final: 73 residues processed: 191 average time/residue: 0.3961 time to fit residues: 132.0991 Evaluate side-chains 187 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 102 time to evaluate : 4.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1146 ASP Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 237 optimal weight: 0.9990 chunk 381 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 181 optimal weight: 40.0000 chunk 265 optimal weight: 9.9990 chunk 400 optimal weight: 30.0000 chunk 368 optimal weight: 10.0000 chunk 318 optimal weight: 0.2980 chunk 33 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 32669 Z= 0.160 Angle : 0.538 14.712 44474 Z= 0.266 Chirality : 0.044 0.381 5135 Planarity : 0.003 0.046 5703 Dihedral : 6.038 58.965 5283 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 2.39 % Allowed : 17.72 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3997 helix: 2.42 (0.21), residues: 681 sheet: 0.14 (0.16), residues: 995 loop : -0.74 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 97 HIS 0.002 0.000 HIS C 655 PHE 0.021 0.001 PHE F 67 TYR 0.012 0.001 TYR A 369 ARG 0.014 0.000 ARG B 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 109 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8819 (pp30) REVERT: A 52 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8338 (tp40) REVERT: A 298 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8438 (tm-30) REVERT: A 354 ASN cc_start: 0.9481 (p0) cc_final: 0.9272 (p0) REVERT: A 540 ASN cc_start: 0.2305 (OUTLIER) cc_final: 0.1698 (t0) REVERT: A 612 TYR cc_start: 0.9071 (m-80) cc_final: 0.8524 (m-80) REVERT: A 627 ASP cc_start: 0.9442 (OUTLIER) cc_final: 0.9164 (p0) REVERT: A 697 MET cc_start: 0.9363 (ttm) cc_final: 0.8823 (ttm) REVERT: A 820 ASP cc_start: 0.9560 (OUTLIER) cc_final: 0.9151 (m-30) REVERT: H 3 GLN cc_start: 0.9035 (mm110) cc_final: 0.8587 (mm-40) REVERT: B 275 PHE cc_start: 0.9337 (OUTLIER) cc_final: 0.9015 (m-80) REVERT: B 584 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8458 (tp) REVERT: B 697 MET cc_start: 0.9123 (mmm) cc_final: 0.8864 (mmm) REVERT: B 900 MET cc_start: 0.9403 (mmt) cc_final: 0.8971 (mmt) REVERT: B 1083 HIS cc_start: 0.8528 (OUTLIER) cc_final: 0.8276 (t-90) REVERT: C 759 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8775 (t80) REVERT: D 34 MET cc_start: 0.9407 (tpt) cc_final: 0.8644 (tpp) REVERT: D 100 PHE cc_start: 0.8538 (m-80) cc_final: 0.8194 (t80) REVERT: F 18 VAL cc_start: 0.7137 (OUTLIER) cc_final: 0.6937 (p) REVERT: F 34 MET cc_start: 0.9422 (OUTLIER) cc_final: 0.8980 (tpt) outliers start: 83 outliers final: 66 residues processed: 186 average time/residue: 0.4038 time to fit residues: 129.2779 Evaluate side-chains 181 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 103 time to evaluate : 3.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 253 optimal weight: 9.9990 chunk 339 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 294 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 319 optimal weight: 0.3980 chunk 133 optimal weight: 9.9990 chunk 327 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.044389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.028281 restraints weight = 228737.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.029355 restraints weight = 111814.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.029985 restraints weight = 72126.365| |-----------------------------------------------------------------------------| r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32669 Z= 0.287 Angle : 0.584 14.559 44474 Z= 0.290 Chirality : 0.043 0.376 5135 Planarity : 0.004 0.045 5703 Dihedral : 6.057 58.597 5283 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.27 % Rotamer: Outliers : 2.50 % Allowed : 17.52 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3997 helix: 2.41 (0.21), residues: 681 sheet: 0.13 (0.16), residues: 999 loop : -0.78 (0.13), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 258 HIS 0.003 0.001 HIS C 655 PHE 0.022 0.001 PHE H 67 TYR 0.012 0.001 TYR B 904 ARG 0.012 0.000 ARG B 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4841.98 seconds wall clock time: 91 minutes 0.02 seconds (5460.02 seconds total)