Starting phenix.real_space_refine on Wed Mar 20 00:22:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg9_32481/03_2024/7wg9_32481.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg9_32481/03_2024/7wg9_32481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg9_32481/03_2024/7wg9_32481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg9_32481/03_2024/7wg9_32481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg9_32481/03_2024/7wg9_32481.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg9_32481/03_2024/7wg9_32481.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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 117 5.16 5 C 16388 2.51 5 N 4228 2.21 5 O 5036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1137": "OD1" <-> "OD2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 617": "OE1" <-> "OE2" Residue "C PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1087": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1109": "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: 25769 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Chain: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "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: "L" 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: "P" 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 13.62, per 1000 atoms: 0.53 Number of scatterers: 25769 At special positions: 0 Unit cell: (141.24, 146.59, 200.09, 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 117 16.00 O 5036 8.00 N 4228 7.00 C 16388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.04 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.02 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 647 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.02 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 647 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 280 " " NAG A1304 " - " ASN A 329 " " NAG A1305 " - " ASN A 341 " " NAG A1306 " - " ASN A 601 " " NAG A1307 " - " ASN A 614 " " NAG A1308 " - " ASN A 655 " " NAG A1309 " - " ASN A 707 " " NAG A1310 " - " ASN A1072 " " NAG A1311 " - " ASN A 163 " " NAG A1312 " - " ASN A 232 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 280 " " NAG B1304 " - " ASN B 329 " " NAG B1305 " - " ASN B 341 " " NAG B1306 " - " ASN B 614 " " NAG B1307 " - " ASN B 655 " " NAG B1308 " - " ASN B 707 " " NAG B1309 " - " ASN B1072 " " NAG B1310 " - " ASN B 163 " " NAG B1311 " - " ASN B 601 " " NAG B1312 " - " ASN B 232 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 280 " " NAG C1304 " - " ASN C 329 " " NAG C1305 " - " ASN C 341 " " NAG C1306 " - " ASN C 614 " " NAG C1307 " - " ASN C 655 " " NAG C1308 " - " ASN C1072 " " NAG C1309 " - " ASN C 163 " " NAG C1310 " - " ASN C 232 " " NAG C1311 " - " ASN C 601 " " NAG D 1 " - " ASN A 715 " " NAG E 1 " - " ASN A 799 " " NAG F 1 " - " ASN A1096 " " NAG G 1 " - " ASN A1132 " " NAG H 1 " - " ASN B 715 " " NAG I 1 " - " ASN B 799 " " NAG J 1 " - " ASN B1096 " " NAG K 1 " - " ASN B1132 " " NAG L 1 " - " ASN C 707 " " NAG M 1 " - " ASN C 715 " " NAG N 1 " - " ASN C 799 " " NAG O 1 " - " ASN C1096 " " NAG P 1 " - " ASN C1132 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.42 Conformation dependent library (CDL) restraints added in 4.7 seconds 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 44 sheets defined 25.4% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.661A pdb=" N HIS A 146 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 147 " --> pdb=" O TYR A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 147' Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.558A pdb=" N VAL A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 614 through 618 removed outlier: 3.689A pdb=" N VAL A 618 " --> pdb=" O CYS A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 741 removed outlier: 3.891A pdb=" N TYR A 739 " --> pdb=" O ASP A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 756 through 781 removed outlier: 3.748A pdb=" N GLN A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 848 through 853 removed outlier: 3.553A pdb=" N LYS A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 883 Processing helix chain 'A' and resid 884 through 889 removed outlier: 4.146A pdb=" N ALA A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 889' Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.879A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 Processing helix chain 'A' and resid 940 through 942 No H-bonds generated for 'chain 'A' and resid 940 through 942' Processing helix chain 'A' and resid 943 through 963 removed outlier: 3.866A pdb=" N VAL A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 982 Processing helix chain 'A' and resid 983 through 1032 removed outlier: 3.743A pdb=" N GLU A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1116 No H-bonds generated for 'chain 'A' and resid 1114 through 1116' Processing helix chain 'A' and resid 1139 through 1146 removed outlier: 4.261A pdb=" N LEU A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 335 through 341 Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.559A pdb=" N TRP B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.061A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 4.234A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 409 " --> pdb=" O ARG B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 618 removed outlier: 3.606A pdb=" N VAL B 618 " --> pdb=" O CYS B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 741 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.564A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 Processing helix chain 'B' and resid 848 through 855 removed outlier: 4.292A pdb=" N LYS B 852 " --> pdb=" O ILE B 848 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN B 854 " --> pdb=" O ALA B 850 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY B 855 " --> pdb=" O GLN B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 882 Processing helix chain 'B' and resid 895 through 908 Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.635A pdb=" N VAL B 913 " --> pdb=" O THR B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 939 Processing helix chain 'B' and resid 940 through 942 No H-bonds generated for 'chain 'B' and resid 940 through 942' Processing helix chain 'B' and resid 943 through 963 removed outlier: 4.339A pdb=" N VAL B 949 " --> pdb=" O LYS B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 982 Processing helix chain 'B' and resid 983 through 1030 removed outlier: 5.144A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1146 removed outlier: 4.655A pdb=" N GLU B1142 " --> pdb=" O PRO B1138 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 335 through 341 removed outlier: 3.918A pdb=" N VAL C 339 " --> pdb=" O PRO C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 removed outlier: 3.738A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.503A pdb=" N LEU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 5.133A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 735 through 741 removed outlier: 3.550A pdb=" N TYR C 739 " --> pdb=" O ASP C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 756 through 781 removed outlier: 4.145A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 761 " --> pdb=" O PHE C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 848 through 852 Processing helix chain 'C' and resid 853 through 855 No H-bonds generated for 'chain 'C' and resid 853 through 855' Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.506A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 908 removed outlier: 3.623A pdb=" N ILE C 907 " --> pdb=" O ARG C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 917 removed outlier: 3.809A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 939 removed outlier: 3.882A pdb=" N THR C 939 " --> pdb=" O SER C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 942 No H-bonds generated for 'chain 'C' and resid 940 through 942' Processing helix chain 'C' and resid 943 through 963 removed outlier: 4.312A pdb=" N VAL C 949 " --> pdb=" O LYS C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 982 removed outlier: 3.549A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 979 " --> pdb=" O LEU C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 986 Processing helix chain 'C' and resid 987 through 1030 Processing helix chain 'C' and resid 1139 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.516A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 96 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASN A 186 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 195 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N PHE A 199 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP A 226 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE A 201 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.663A pdb=" N PHE A 43 " --> pdb=" O PHE B 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.582A pdb=" N GLY A 107 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 11.632A pdb=" N VAL A 126 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 10.285A pdb=" N GLU A 167 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.298A pdb=" N ILE A 128 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N THR A 165 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL A 130 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ASN A 163 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU A 132 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA A 161 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN A 134 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 312 Processing sheet with id=AA6, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 326 removed outlier: 3.508A pdb=" N ARG A 326 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 352 through 356 removed outlier: 3.603A pdb=" N CYS A 430 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 359 through 360 removed outlier: 6.694A pdb=" N CYS A 359 " --> pdb=" O CYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 654 removed outlier: 4.619A pdb=" N THR A 694 " --> pdb=" O VAL A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.907A pdb=" N ALA A 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.828A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN A 715 " --> pdb=" O ALA A1068 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A1054 " --> pdb=" O GLY A1057 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.828A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN A 715 " --> pdb=" O ALA A1068 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 734 Processing sheet with id=AB7, first strand: chain 'A' and resid 1118 through 1123 removed outlier: 4.391A pdb=" N ALA A1085 " --> pdb=" O SER A1121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.661A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU B 96 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN B 186 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 225 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.610A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 317 removed outlier: 4.680A pdb=" N VAL B 593 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASN B 315 " --> pdb=" O GLY B 591 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY B 591 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN B 611 " --> pdb=" O GLY B 592 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.726A pdb=" N ASN B 392 " --> pdb=" O GLU B 514 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 359 through 360 removed outlier: 7.327A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AC6, first strand: chain 'B' and resid 471 through 472 removed outlier: 3.584A pdb=" N TYR B 471 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 487 " --> pdb=" O TYR B 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 537 through 540 Processing sheet with id=AC8, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.022A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 709 through 713 Processing sheet with id=AD1, first strand: chain 'B' and resid 716 through 726 removed outlier: 3.559A pdb=" N MET B1048 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 732 through 734 Processing sheet with id=AD3, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 4.875A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.897A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR C 263 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 227 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 201 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL C 225 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.896A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.805A pdb=" N VAL C 130 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLU C 132 " --> pdb=" O CYS C 164 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N GLN C 134 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N ASN C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 309 through 316 removed outlier: 4.651A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 648 " --> pdb=" O PHE C 641 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 323 through 324 removed outlier: 3.527A pdb=" N ILE C 324 " --> pdb=" O ASN C 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 352 through 356 removed outlier: 3.900A pdb=" N ALA C 433 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR C 374 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE2, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE3, first strand: chain 'C' and resid 549 through 552 Processing sheet with id=AE4, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.084A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 668 " --> pdb=" O ILE C 664 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 709 through 713 Processing sheet with id=AE6, first strand: chain 'C' and resid 716 through 726 removed outlier: 3.648A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AE8, first strand: chain 'C' and resid 1092 through 1095 958 hydrogen bonds defined for protein. 2625 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: 11.58 Time building geometry restraints manager: 11.26 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: 8186 1.34 - 1.47: 6584 1.47 - 1.59: 11424 1.59 - 1.71: 1 1.71 - 1.83: 147 Bond restraints: 26342 Sorted by residual: bond pdb=" CA LEU B 177 " pdb=" C LEU B 177 " ideal model delta sigma weight residual 1.523 1.552 -0.028 1.34e-02 5.57e+03 4.48e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.37e+00 bond pdb=" CB PRO C 525 " pdb=" CG PRO C 525 " ideal model delta sigma weight residual 1.492 1.594 -0.102 5.00e-02 4.00e+02 4.14e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 26337 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.41: 709 106.41 - 113.52: 14599 113.52 - 120.62: 10251 120.62 - 127.73: 10093 127.73 - 134.83: 178 Bond angle restraints: 35830 Sorted by residual: angle pdb=" CA TRP C 152 " pdb=" CB TRP C 152 " pdb=" CG TRP C 152 " ideal model delta sigma weight residual 113.60 120.35 -6.75 1.90e+00 2.77e-01 1.26e+01 angle pdb=" C ALA A 568 " pdb=" N ASP A 569 " pdb=" CA ASP A 569 " ideal model delta sigma weight residual 122.46 127.32 -4.86 1.41e+00 5.03e-01 1.19e+01 angle pdb=" C LYS B 97 " pdb=" N SER B 98 " pdb=" CA SER B 98 " ideal model delta sigma weight residual 121.54 127.34 -5.80 1.91e+00 2.74e-01 9.21e+00 angle pdb=" C ALA C 568 " pdb=" N ASP C 569 " pdb=" CA ASP C 569 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.52e+00 angle pdb=" CA CYS A 536 " pdb=" CB CYS A 536 " pdb=" SG CYS A 536 " ideal model delta sigma weight residual 114.40 121.10 -6.70 2.30e+00 1.89e-01 8.48e+00 ... (remaining 35825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.66: 15087 19.66 - 39.31: 1119 39.31 - 58.97: 226 58.97 - 78.62: 57 78.62 - 98.28: 17 Dihedral angle restraints: 16506 sinusoidal: 7233 harmonic: 9273 Sorted by residual: dihedral pdb=" CB CYS B 289 " pdb=" SG CYS B 289 " pdb=" SG CYS B 299 " pdb=" CB CYS B 299 " ideal model delta sinusoidal sigma weight residual -86.00 -4.64 -81.36 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS B 478 " pdb=" SG CYS B 478 " pdb=" SG CYS B 486 " pdb=" CB CYS B 486 " ideal model delta sinusoidal sigma weight residual 93.00 173.47 -80.47 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS C 478 " pdb=" SG CYS C 478 " pdb=" SG CYS C 486 " pdb=" CB CYS C 486 " ideal model delta sinusoidal sigma weight residual 93.00 149.89 -56.89 1 1.00e+01 1.00e-02 4.36e+01 ... (remaining 16503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 4135 0.112 - 0.225: 84 0.225 - 0.337: 3 0.337 - 0.449: 0 0.449 - 0.562: 1 Chirality restraints: 4223 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN C 707 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.89e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C1096 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C1132 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 4220 not shown) Planarity restraints: 4615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 227 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO C 228 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 228 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 228 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 206 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO B 207 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 227 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO B 228 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 228 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 228 " -0.030 5.00e-02 4.00e+02 ... (remaining 4612 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 632 2.69 - 3.25: 25204 3.25 - 3.80: 39060 3.80 - 4.35: 49159 4.35 - 4.90: 83638 Nonbonded interactions: 197693 Sorted by model distance: nonbonded pdb=" OG SER B 436 " pdb=" OD2 ASP B 440 " model vdw 2.144 2.440 nonbonded pdb=" OG1 THR A 391 " pdb=" O GLU A 514 " model vdw 2.161 2.440 nonbonded pdb=" O PHE B 106 " pdb=" OG SER B 116 " model vdw 2.181 2.440 nonbonded pdb=" NH1 ARG C1017 " pdb=" OD1 ASN C1021 " model vdw 2.211 2.520 nonbonded pdb=" O ASP B 440 " pdb=" ND2 ASN B 446 " model vdw 2.212 2.520 ... (remaining 197688 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 1146 or resid 1301 through 1311)) selection = (chain 'B' and (resid 14 through 1146 or resid 1301 through 1311)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.420 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 69.630 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.270 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 26342 Z= 0.225 Angle : 0.615 9.831 35830 Z= 0.312 Chirality : 0.046 0.562 4223 Planarity : 0.004 0.073 4567 Dihedral : 14.257 98.277 10416 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3153 helix: 1.64 (0.21), residues: 662 sheet: -0.22 (0.20), residues: 625 loop : -1.62 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.004 0.001 HIS B 146 PHE 0.015 0.001 PHE A 390 TYR 0.019 0.001 TYR B 168 ARG 0.007 0.000 ARG B 326 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 499 time to evaluate : 2.651 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: A 118 LEU cc_start: 0.8813 (tp) cc_final: 0.8570 (tp) REVERT: A 168 TYR cc_start: 0.8385 (t80) cc_final: 0.8172 (t80) REVERT: A 554 ASN cc_start: 0.7887 (p0) cc_final: 0.7584 (p0) REVERT: A 582 ILE cc_start: 0.8426 (mm) cc_final: 0.8217 (mm) REVERT: A 882 SER cc_start: 0.9008 (m) cc_final: 0.8801 (p) REVERT: A 974 VAL cc_start: 0.8850 (t) cc_final: 0.8513 (t) REVERT: B 79 PHE cc_start: 0.6721 (t80) cc_final: 0.6424 (t80) REVERT: B 135 PHE cc_start: 0.8092 (m-80) cc_final: 0.7611 (m-80) REVERT: B 264 TYR cc_start: 0.6882 (m-80) cc_final: 0.6628 (m-80) REVERT: B 368 ASN cc_start: 0.8440 (m-40) cc_final: 0.7394 (p0) REVERT: B 386 ASN cc_start: 0.8020 (m-40) cc_final: 0.7582 (p0) REVERT: B 416 ILE cc_start: 0.8794 (pt) cc_final: 0.8512 (pt) REVERT: B 435 ASN cc_start: 0.7739 (t0) cc_final: 0.6771 (m-40) REVERT: B 491 GLN cc_start: 0.7412 (tm-30) cc_final: 0.7066 (tm-30) REVERT: B 527 LYS cc_start: 0.7961 (mmtm) cc_final: 0.7680 (mtmt) REVERT: B 705 TYR cc_start: 0.7322 (t80) cc_final: 0.6739 (t80) REVERT: B 778 GLU cc_start: 0.7715 (tt0) cc_final: 0.7462 (pt0) REVERT: B 867 MET cc_start: 0.8509 (mtt) cc_final: 0.8255 (mtt) REVERT: B 915 TYR cc_start: 0.8544 (m-80) cc_final: 0.8212 (m-10) REVERT: B 1111 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8166 (mt0) REVERT: C 240 LEU cc_start: 0.7360 (pt) cc_final: 0.7052 (pp) REVERT: C 352 ASN cc_start: 0.7361 (t0) cc_final: 0.6430 (p0) REVERT: C 898 MET cc_start: 0.7490 (mtt) cc_final: 0.7244 (mtt) outliers start: 0 outliers final: 0 residues processed: 499 average time/residue: 0.3776 time to fit residues: 291.6916 Evaluate side-chains 222 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 82 optimal weight: 0.0770 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 50.0000 chunk 249 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN C 134 GLN C 392 ASN C 899 GLN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 26342 Z= 0.326 Angle : 0.664 10.115 35830 Z= 0.332 Chirality : 0.047 0.446 4223 Planarity : 0.004 0.058 4567 Dihedral : 8.377 82.967 4698 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.27 % Allowed : 8.95 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3153 helix: 1.91 (0.20), residues: 674 sheet: -0.23 (0.21), residues: 577 loop : -1.67 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 434 HIS 0.008 0.001 HIS B 653 PHE 0.018 0.002 PHE B 904 TYR 0.019 0.001 TYR B1065 ARG 0.006 0.001 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 244 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.9020 (mm) cc_final: 0.8641 (mt) REVERT: A 152 TRP cc_start: 0.5482 (t-100) cc_final: 0.5243 (t-100) REVERT: A 153 MET cc_start: 0.6533 (mpp) cc_final: 0.5889 (pmm) REVERT: A 853 PHE cc_start: 0.7720 (m-10) cc_final: 0.7495 (m-80) REVERT: A 882 SER cc_start: 0.9181 (m) cc_final: 0.8912 (p) REVERT: A 975 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7754 (mp) REVERT: A 1029 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7105 (mt-10) REVERT: B 135 PHE cc_start: 0.7685 (m-80) cc_final: 0.7146 (m-80) REVERT: B 264 TYR cc_start: 0.7013 (m-80) cc_final: 0.6707 (m-80) REVERT: B 705 TYR cc_start: 0.7852 (t80) cc_final: 0.7184 (t80) REVERT: B 867 MET cc_start: 0.8744 (mtt) cc_final: 0.8529 (mtm) REVERT: B 915 TYR cc_start: 0.8698 (m-80) cc_final: 0.8095 (m-10) REVERT: B 974 VAL cc_start: 0.8629 (t) cc_final: 0.8396 (t) REVERT: B 977 ASP cc_start: 0.7496 (t0) cc_final: 0.7279 (t0) REVERT: B 1111 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8182 (mt0) REVERT: C 352 ASN cc_start: 0.7351 (t0) cc_final: 0.6425 (p0) REVERT: C 376 LYS cc_start: 0.8844 (mtpp) cc_final: 0.8558 (ttpp) REVERT: C 390 PHE cc_start: 0.8571 (m-10) cc_final: 0.8261 (m-80) REVERT: C 898 MET cc_start: 0.7994 (mtt) cc_final: 0.7758 (mtt) REVERT: C 902 TYR cc_start: 0.7249 (m-10) cc_final: 0.7003 (m-10) REVERT: C 1048 MET cc_start: 0.8022 (ptt) cc_final: 0.7776 (ptt) outliers start: 63 outliers final: 38 residues processed: 287 average time/residue: 0.3417 time to fit residues: 159.3341 Evaluate side-chains 238 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 198 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 773 ASP Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 919 LYS Chi-restraints excluded: chain C residue 967 ASN Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1008 GLN Chi-restraints excluded: chain C residue 1028 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 312 optimal weight: 3.9990 chunk 257 optimal weight: 0.8980 chunk 286 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 ASN ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 ASN ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN B 923 ASN ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 924 GLN ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1086 HIS ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1104 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 26342 Z= 0.301 Angle : 0.619 10.069 35830 Z= 0.309 Chirality : 0.046 0.442 4223 Planarity : 0.004 0.063 4567 Dihedral : 7.799 76.754 4698 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.55 % Allowed : 12.26 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.14), residues: 3153 helix: 1.97 (0.20), residues: 664 sheet: -0.14 (0.21), residues: 564 loop : -1.71 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 884 HIS 0.007 0.001 HIS C1062 PHE 0.025 0.002 PHE C 560 TYR 0.018 0.001 TYR B1065 ARG 0.006 0.000 ARG B 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 212 time to evaluate : 2.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.9191 (mm) cc_final: 0.8892 (mt) REVERT: A 882 SER cc_start: 0.9198 (m) cc_final: 0.8943 (p) REVERT: A 952 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7611 (mt0) REVERT: A 1029 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7051 (mt-10) REVERT: B 135 PHE cc_start: 0.7669 (m-80) cc_final: 0.7156 (m-80) REVERT: B 200 LYS cc_start: 0.7589 (mttp) cc_final: 0.7326 (mtmt) REVERT: B 264 TYR cc_start: 0.6964 (m-80) cc_final: 0.6674 (m-80) REVERT: B 876 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8098 (tt) REVERT: B 955 GLN cc_start: 0.8325 (tp40) cc_final: 0.8117 (tt0) REVERT: B 977 ASP cc_start: 0.7759 (t0) cc_final: 0.7539 (t0) REVERT: B 1029 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: B 1111 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8196 (mt0) REVERT: C 325 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8141 (t) REVERT: C 448 ASN cc_start: 0.7545 (OUTLIER) cc_final: 0.6953 (m110) REVERT: C 880 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8878 (mp) REVERT: C 898 MET cc_start: 0.7873 (mtt) cc_final: 0.7667 (mtp) REVERT: C 902 TYR cc_start: 0.7328 (m-10) cc_final: 0.7124 (m-10) outliers start: 71 outliers final: 42 residues processed: 261 average time/residue: 0.3387 time to fit residues: 144.8838 Evaluate side-chains 240 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 191 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 773 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 996 THR Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 560 PHE Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 967 ASN Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1003 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 32 optimal weight: 30.0000 chunk 138 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 307 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 171 GLN A 802 GLN A 933 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 911 GLN ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN C1056 HIS ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 26342 Z= 0.331 Angle : 0.635 9.911 35830 Z= 0.317 Chirality : 0.047 0.444 4223 Planarity : 0.004 0.065 4567 Dihedral : 7.388 66.102 4698 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.74 % Allowed : 13.52 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.92 (0.14), residues: 3153 helix: 1.85 (0.20), residues: 658 sheet: -0.19 (0.20), residues: 610 loop : -1.76 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 884 HIS 0.007 0.001 HIS C1062 PHE 0.027 0.002 PHE B 853 TYR 0.021 0.002 TYR C 168 ARG 0.006 0.001 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 224 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.9198 (mm) cc_final: 0.8877 (mt) REVERT: A 135 PHE cc_start: 0.7984 (m-80) cc_final: 0.7742 (m-10) REVERT: A 153 MET cc_start: 0.5987 (mpp) cc_final: 0.5476 (pmm) REVERT: A 882 SER cc_start: 0.9221 (m) cc_final: 0.9000 (p) REVERT: A 952 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7608 (mt0) REVERT: A 1029 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: B 135 PHE cc_start: 0.7676 (m-80) cc_final: 0.7185 (m-80) REVERT: B 200 LYS cc_start: 0.7554 (mttp) cc_final: 0.7292 (mtmt) REVERT: B 264 TYR cc_start: 0.6914 (m-80) cc_final: 0.6633 (m-80) REVERT: B 296 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: B 876 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8120 (tt) REVERT: B 986 GLU cc_start: 0.7598 (tp30) cc_final: 0.7324 (tp30) REVERT: B 1029 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: B 1111 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8202 (mt0) REVERT: C 49 HIS cc_start: 0.7934 (t-170) cc_final: 0.7710 (t70) REVERT: C 325 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8256 (t) REVERT: C 327 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6015 (t80) REVERT: C 448 ASN cc_start: 0.7430 (OUTLIER) cc_final: 0.6815 (m110) REVERT: C 527 LYS cc_start: 0.7014 (tptt) cc_final: 0.6759 (mmtm) REVERT: C 547 THR cc_start: 0.8409 (p) cc_final: 0.8175 (p) REVERT: C 576 ASP cc_start: 0.8054 (t0) cc_final: 0.7749 (t0) outliers start: 104 outliers final: 54 residues processed: 307 average time/residue: 0.3354 time to fit residues: 167.7836 Evaluate side-chains 263 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 201 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 773 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 996 THR Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 943 LEU Chi-restraints excluded: chain C residue 967 ASN Chi-restraints excluded: chain C residue 973 SER Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1008 GLN Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 262 optimal weight: 0.3980 chunk 212 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 156 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 386 ASN A 924 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1140 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 26342 Z= 0.320 Angle : 0.625 11.371 35830 Z= 0.312 Chirality : 0.046 0.460 4223 Planarity : 0.004 0.065 4567 Dihedral : 7.211 59.664 4698 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.24 % Allowed : 15.82 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.94 (0.14), residues: 3153 helix: 1.86 (0.20), residues: 659 sheet: -0.25 (0.20), residues: 600 loop : -1.77 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 884 HIS 0.007 0.001 HIS C1062 PHE 0.020 0.002 PHE B 853 TYR 0.018 0.001 TYR B1065 ARG 0.009 0.000 ARG C 353 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 209 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.9212 (mm) cc_final: 0.8892 (mt) REVERT: A 153 MET cc_start: 0.6134 (mpp) cc_final: 0.5529 (pmm) REVERT: A 363 TYR cc_start: 0.8314 (m-80) cc_final: 0.8015 (m-80) REVERT: A 952 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7621 (mt0) REVERT: A 1029 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7060 (mt-10) REVERT: A 1105 ARG cc_start: 0.7483 (mtt90) cc_final: 0.7254 (mtt90) REVERT: B 135 PHE cc_start: 0.7697 (m-80) cc_final: 0.7212 (m-80) REVERT: B 162 ASN cc_start: 0.7494 (OUTLIER) cc_final: 0.7100 (t0) REVERT: B 200 LYS cc_start: 0.7562 (mttp) cc_final: 0.7297 (mtmt) REVERT: B 264 TYR cc_start: 0.6852 (m-80) cc_final: 0.6554 (m-80) REVERT: B 523 CYS cc_start: 0.6231 (OUTLIER) cc_final: 0.5735 (m) REVERT: B 561 GLN cc_start: 0.6593 (OUTLIER) cc_final: 0.6320 (mm-40) REVERT: B 579 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.8011 (p) REVERT: B 853 PHE cc_start: 0.7220 (m-10) cc_final: 0.6926 (m-10) REVERT: B 876 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8126 (tt) REVERT: B 955 GLN cc_start: 0.8392 (tp40) cc_final: 0.8067 (tt0) REVERT: B 986 GLU cc_start: 0.7605 (tp30) cc_final: 0.7318 (tp30) REVERT: B 1029 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: B 1111 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8159 (mt0) REVERT: C 49 HIS cc_start: 0.7934 (t-170) cc_final: 0.7696 (t-170) REVERT: C 327 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6119 (t80) REVERT: C 390 PHE cc_start: 0.8813 (m-80) cc_final: 0.8460 (m-80) REVERT: C 448 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.6778 (m110) REVERT: C 576 ASP cc_start: 0.8051 (t0) cc_final: 0.7690 (t0) REVERT: C 880 ILE cc_start: 0.9093 (mt) cc_final: 0.8849 (mp) outliers start: 90 outliers final: 57 residues processed: 280 average time/residue: 0.3303 time to fit residues: 152.2922 Evaluate side-chains 264 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 197 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 773 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 996 THR Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 967 ASN Chi-restraints excluded: chain C residue 973 SER Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 307 optimal weight: 0.8980 chunk 255 optimal weight: 0.0980 chunk 142 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1140 GLN C 438 ASN ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26342 Z= 0.235 Angle : 0.592 10.034 35830 Z= 0.293 Chirality : 0.045 0.456 4223 Planarity : 0.004 0.064 4567 Dihedral : 6.978 59.614 4698 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.16 % Allowed : 16.40 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.78 (0.14), residues: 3153 helix: 1.96 (0.20), residues: 672 sheet: -0.12 (0.21), residues: 591 loop : -1.68 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 884 HIS 0.005 0.001 HIS C 205 PHE 0.021 0.001 PHE A 92 TYR 0.017 0.001 TYR B1065 ARG 0.005 0.000 ARG B 565 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 202 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.9230 (mm) cc_final: 0.8905 (mt) REVERT: A 153 MET cc_start: 0.5918 (mpp) cc_final: 0.5432 (pmm) REVERT: A 363 TYR cc_start: 0.8272 (m-80) cc_final: 0.8010 (m-80) REVERT: A 952 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7586 (mt0) REVERT: A 1029 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7032 (mt-10) REVERT: A 1108 TYR cc_start: 0.8816 (t80) cc_final: 0.8603 (t80) REVERT: B 135 PHE cc_start: 0.7699 (m-80) cc_final: 0.7231 (m-80) REVERT: B 188 ARG cc_start: 0.5358 (mtm110) cc_final: 0.5036 (mtm180) REVERT: B 200 LYS cc_start: 0.7538 (mttp) cc_final: 0.7122 (mtmt) REVERT: B 264 TYR cc_start: 0.6882 (m-80) cc_final: 0.6607 (m-80) REVERT: B 579 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.8016 (p) REVERT: B 876 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8105 (tt) REVERT: B 955 GLN cc_start: 0.8345 (tp40) cc_final: 0.8084 (tt0) REVERT: B 986 GLU cc_start: 0.7637 (tp30) cc_final: 0.7247 (tp30) REVERT: B 1029 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: B 1111 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8166 (mt0) REVERT: C 49 HIS cc_start: 0.7911 (t-170) cc_final: 0.7670 (t-170) REVERT: C 325 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8175 (t) REVERT: C 327 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.6223 (t80) REVERT: C 390 PHE cc_start: 0.8816 (m-80) cc_final: 0.8478 (m-80) REVERT: C 448 ASN cc_start: 0.7401 (OUTLIER) cc_final: 0.6835 (m110) REVERT: C 527 LYS cc_start: 0.6796 (mmtm) cc_final: 0.6344 (mmtm) REVERT: C 576 ASP cc_start: 0.8053 (t0) cc_final: 0.7703 (t0) REVERT: C 880 ILE cc_start: 0.9078 (mt) cc_final: 0.8844 (mp) REVERT: C 902 TYR cc_start: 0.7393 (m-10) cc_final: 0.7091 (m-10) outliers start: 88 outliers final: 59 residues processed: 270 average time/residue: 0.3374 time to fit residues: 149.7592 Evaluate side-chains 257 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 190 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 992 ASP Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 557 PHE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 967 ASN Chi-restraints excluded: chain C residue 973 SER Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 175 optimal weight: 0.6980 chunk 224 optimal weight: 0.0070 chunk 174 optimal weight: 0.9990 chunk 259 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 306 optimal weight: 0.9980 chunk 191 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 870 GLN C 899 GLN ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26342 Z= 0.159 Angle : 0.560 9.978 35830 Z= 0.274 Chirality : 0.045 0.461 4223 Planarity : 0.004 0.063 4567 Dihedral : 6.615 57.597 4698 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.45 % Allowed : 17.15 % Favored : 80.40 % 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: -0.53 (0.15), residues: 3153 helix: 2.32 (0.20), residues: 673 sheet: 0.04 (0.21), residues: 592 loop : -1.58 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 434 HIS 0.005 0.001 HIS C 205 PHE 0.021 0.001 PHE A 92 TYR 0.015 0.001 TYR B1065 ARG 0.004 0.000 ARG B 565 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 219 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.9213 (mm) cc_final: 0.8909 (mt) REVERT: A 363 TYR cc_start: 0.8253 (m-80) cc_final: 0.8039 (m-80) REVERT: A 1029 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.6993 (mt-10) REVERT: B 135 PHE cc_start: 0.7675 (m-80) cc_final: 0.7207 (m-80) REVERT: B 162 ASN cc_start: 0.7491 (OUTLIER) cc_final: 0.7095 (t0) REVERT: B 264 TYR cc_start: 0.6821 (m-80) cc_final: 0.6537 (m-80) REVERT: B 579 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7933 (p) REVERT: B 955 GLN cc_start: 0.8250 (tp40) cc_final: 0.8046 (tt0) REVERT: B 986 GLU cc_start: 0.7616 (tp30) cc_final: 0.7341 (tp30) REVERT: B 1029 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: B 1111 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8137 (mt0) REVERT: C 51 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8262 (t) REVERT: C 327 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6416 (t80) REVERT: C 390 PHE cc_start: 0.8782 (m-80) cc_final: 0.8462 (m-80) REVERT: C 448 ASN cc_start: 0.7306 (OUTLIER) cc_final: 0.6776 (m110) REVERT: C 576 ASP cc_start: 0.8065 (t0) cc_final: 0.7718 (t0) outliers start: 68 outliers final: 45 residues processed: 271 average time/residue: 0.3131 time to fit residues: 142.0491 Evaluate side-chains 250 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 198 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 992 ASP Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 557 PHE Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 967 ASN Chi-restraints excluded: chain C residue 973 SER Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.7980 chunk 122 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 151 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 240 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1140 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26342 Z= 0.184 Angle : 0.578 10.127 35830 Z= 0.282 Chirality : 0.045 0.461 4223 Planarity : 0.004 0.064 4567 Dihedral : 6.461 57.823 4698 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.41 % Allowed : 17.73 % Favored : 79.86 % 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: -0.47 (0.15), residues: 3153 helix: 2.37 (0.20), residues: 672 sheet: 0.07 (0.21), residues: 600 loop : -1.55 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 64 HIS 0.011 0.001 HIS C 49 PHE 0.021 0.001 PHE A 92 TYR 0.015 0.001 TYR B1065 ARG 0.005 0.000 ARG B 565 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 201 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.9198 (mm) cc_final: 0.8875 (mt) REVERT: A 363 TYR cc_start: 0.8256 (m-80) cc_final: 0.8047 (m-80) REVERT: A 853 PHE cc_start: 0.7574 (m-10) cc_final: 0.7183 (m-80) REVERT: A 1029 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6938 (mt-10) REVERT: B 135 PHE cc_start: 0.7689 (m-80) cc_final: 0.7215 (m-80) REVERT: B 162 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.7054 (t0) REVERT: B 200 LYS cc_start: 0.7565 (mttp) cc_final: 0.7296 (mtmt) REVERT: B 264 TYR cc_start: 0.6781 (m-80) cc_final: 0.6507 (m-80) REVERT: B 579 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7868 (p) REVERT: B 955 GLN cc_start: 0.8254 (tp40) cc_final: 0.8052 (tt0) REVERT: B 986 GLU cc_start: 0.7632 (tp30) cc_final: 0.7292 (tp30) REVERT: B 1029 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: B 1111 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8146 (mt0) REVERT: C 325 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8177 (t) REVERT: C 327 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6541 (t80) REVERT: C 390 PHE cc_start: 0.8822 (m-80) cc_final: 0.8609 (m-80) REVERT: C 448 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.7096 (m110) REVERT: C 576 ASP cc_start: 0.8104 (t0) cc_final: 0.7755 (t0) REVERT: C 1048 MET cc_start: 0.8022 (ptt) cc_final: 0.7748 (ptt) outliers start: 67 outliers final: 52 residues processed: 250 average time/residue: 0.3219 time to fit residues: 134.7563 Evaluate side-chains 252 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 193 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 992 ASP Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 557 PHE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 967 ASN Chi-restraints excluded: chain C residue 973 SER Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 285 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 224 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 258 optimal weight: 20.0000 chunk 270 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1003 GLN ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26342 Z= 0.233 Angle : 0.595 12.265 35830 Z= 0.292 Chirality : 0.045 0.465 4223 Planarity : 0.004 0.064 4567 Dihedral : 6.409 57.913 4698 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.73 % Allowed : 17.80 % Favored : 79.47 % 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: -0.55 (0.15), residues: 3153 helix: 2.31 (0.20), residues: 665 sheet: -0.01 (0.21), residues: 602 loop : -1.58 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.009 0.001 HIS C 49 PHE 0.024 0.001 PHE C 560 TYR 0.016 0.001 TYR B 871 ARG 0.005 0.000 ARG B 565 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 204 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.9209 (mm) cc_final: 0.8898 (mt) REVERT: A 853 PHE cc_start: 0.7535 (m-10) cc_final: 0.7177 (m-80) REVERT: A 1029 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6914 (mt-10) REVERT: B 135 PHE cc_start: 0.7579 (m-80) cc_final: 0.7113 (m-80) REVERT: B 162 ASN cc_start: 0.7497 (OUTLIER) cc_final: 0.7042 (t0) REVERT: B 175 MET cc_start: 0.3344 (pmm) cc_final: 0.1963 (pmm) REVERT: B 200 LYS cc_start: 0.7647 (mttp) cc_final: 0.7357 (mtmt) REVERT: B 264 TYR cc_start: 0.6786 (m-80) cc_final: 0.6513 (m-80) REVERT: B 579 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7851 (p) REVERT: B 955 GLN cc_start: 0.8268 (tp40) cc_final: 0.8061 (tt0) REVERT: B 986 GLU cc_start: 0.7647 (tp30) cc_final: 0.7204 (tp30) REVERT: B 1029 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: B 1111 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8182 (mt0) REVERT: C 327 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.6544 (t80) REVERT: C 448 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7199 (m110) REVERT: C 576 ASP cc_start: 0.8114 (t0) cc_final: 0.7733 (t0) REVERT: C 880 ILE cc_start: 0.9123 (mp) cc_final: 0.8917 (mp) REVERT: C 999 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8459 (tp) REVERT: C 1048 MET cc_start: 0.8124 (ptt) cc_final: 0.7812 (ptt) outliers start: 76 outliers final: 60 residues processed: 259 average time/residue: 0.3374 time to fit residues: 145.0370 Evaluate side-chains 264 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 197 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 992 ASP Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 557 PHE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 967 ASN Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1003 GLN Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.8980 chunk 302 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 209 optimal weight: 5.9990 chunk 316 optimal weight: 0.6980 chunk 291 optimal weight: 0.7980 chunk 252 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1003 GLN ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26342 Z= 0.179 Angle : 0.590 12.035 35830 Z= 0.286 Chirality : 0.045 0.463 4223 Planarity : 0.004 0.065 4567 Dihedral : 6.292 57.774 4698 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.41 % Allowed : 18.05 % Favored : 79.54 % 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: -0.46 (0.15), residues: 3153 helix: 2.42 (0.20), residues: 666 sheet: 0.03 (0.20), residues: 610 loop : -1.54 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.009 0.001 HIS C 49 PHE 0.028 0.001 PHE A 372 TYR 0.017 0.001 TYR C 168 ARG 0.004 0.000 ARG B 565 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 208 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.9217 (mm) cc_final: 0.8897 (mt) REVERT: A 1029 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6883 (mt-10) REVERT: B 135 PHE cc_start: 0.7508 (m-80) cc_final: 0.7053 (m-80) REVERT: B 162 ASN cc_start: 0.7494 (OUTLIER) cc_final: 0.7045 (t0) REVERT: B 175 MET cc_start: 0.3510 (pmm) cc_final: 0.2185 (pmm) REVERT: B 200 LYS cc_start: 0.7590 (mttp) cc_final: 0.7338 (mtmt) REVERT: B 264 TYR cc_start: 0.6753 (m-80) cc_final: 0.6478 (m-80) REVERT: B 394 TYR cc_start: 0.7648 (m-80) cc_final: 0.7268 (m-10) REVERT: B 579 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7887 (p) REVERT: B 986 GLU cc_start: 0.7554 (tp30) cc_final: 0.7267 (tp30) REVERT: B 1029 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: B 1111 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8168 (mt0) REVERT: C 327 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.6641 (t80) REVERT: C 448 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7270 (m110) REVERT: C 576 ASP cc_start: 0.8104 (t0) cc_final: 0.7724 (t0) REVERT: C 880 ILE cc_start: 0.9122 (mp) cc_final: 0.8899 (mp) REVERT: C 1048 MET cc_start: 0.7981 (ptt) cc_final: 0.7688 (ptt) outliers start: 67 outliers final: 57 residues processed: 261 average time/residue: 0.3308 time to fit residues: 142.4243 Evaluate side-chains 258 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 195 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 992 ASP Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 557 PHE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 967 ASN Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1003 GLN Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 3.9990 chunk 268 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 232 optimal weight: 0.6980 chunk 37 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN B 772 GLN ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1003 GLN ** C1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.167992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106437 restraints weight = 40678.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.108590 restraints weight = 23700.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.108822 restraints weight = 15949.586| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 26342 Z= 0.400 Angle : 0.686 10.415 35830 Z= 0.341 Chirality : 0.048 0.470 4223 Planarity : 0.004 0.065 4567 Dihedral : 6.624 58.119 4698 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.59 % Allowed : 18.19 % Favored : 79.22 % 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: -0.88 (0.14), residues: 3153 helix: 1.64 (0.20), residues: 690 sheet: -0.12 (0.20), residues: 618 loop : -1.72 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 884 HIS 0.011 0.001 HIS C 49 PHE 0.030 0.002 PHE A 372 TYR 0.019 0.002 TYR B1065 ARG 0.005 0.001 ARG C1105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4604.38 seconds wall clock time: 84 minutes 45.78 seconds (5085.78 seconds total)