Starting phenix.real_space_refine on Tue Feb 20 06:08:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3w_35160/02_2024/8i3w_35160.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3w_35160/02_2024/8i3w_35160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3w_35160/02_2024/8i3w_35160.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3w_35160/02_2024/8i3w_35160.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3w_35160/02_2024/8i3w_35160.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3w_35160/02_2024/8i3w_35160.pdb" } resolution = 2.8 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= 0.003 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 123 5.16 5 C 17127 2.51 5 N 4419 2.21 5 O 5331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 394": "OD1" <-> "OD2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 582": "OD1" <-> "OD2" Residue "A TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A ASP 788": "OD1" <-> "OD2" Residue "A PHE 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 283": "OD1" <-> "OD2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 570": "OD1" <-> "OD2" Residue "B PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 767": "OD1" <-> "OD2" Residue "B PHE 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 971": "OD1" <-> "OD2" Residue "B PHE 1113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C ASP 283": "OD1" <-> "OD2" Residue "C ASP 320": "OD1" <-> "OD2" Residue "C TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 564": "OD1" <-> "OD2" Residue "C ASP 570": "OD1" <-> "OD2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 767": "OD1" <-> "OD2" Residue "C ASP 928": "OD1" <-> "OD2" Residue "C GLU 1009": "OE1" <-> "OE2" Residue "C PHE 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27000 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8678 Classifications: {'peptide': 1115} Link IDs: {'PTRANS': 51, 'TRANS': 1063} Chain: "B" Number of atoms: 8678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8678 Classifications: {'peptide': 1115} Link IDs: {'PTRANS': 51, 'TRANS': 1063} Chain: "C" Number of atoms: 8678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8678 Classifications: {'peptide': 1115} Link IDs: {'PTRANS': 51, 'TRANS': 1063} 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: "Q" 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 15.37, per 1000 atoms: 0.57 Number of scatterers: 27000 At special positions: 0 Unit cell: (150.8, 144.56, 160.16, 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 123 16.00 O 5331 8.00 N 4419 7.00 C 17127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 297 " distance=2.02 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 428 " distance=2.05 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 484 " distance=2.02 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 645 " distance=2.03 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 667 " distance=2.03 Simple disulfide: pdb=" SG CYS A 730 " - pdb=" SG CYS A 752 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 741 " distance=2.03 Simple disulfide: pdb=" SG CYS A 832 " - pdb=" SG CYS A 843 " distance=2.03 Simple disulfide: pdb=" SG CYS A1024 " - pdb=" SG CYS A1035 " distance=2.03 Simple disulfide: pdb=" SG CYS A1074 " - pdb=" SG CYS A1118 " distance=1.68 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 297 " distance=2.02 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 484 " distance=2.02 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Simple disulfide: pdb=" SG CYS B 730 " - pdb=" SG CYS B 752 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 741 " distance=2.03 Simple disulfide: pdb=" SG CYS B 832 " - pdb=" SG CYS B 843 " distance=2.03 Simple disulfide: pdb=" SG CYS B1024 " - pdb=" SG CYS B1035 " distance=2.03 Simple disulfide: pdb=" SG CYS B1074 " - pdb=" SG CYS B1118 " distance=1.15 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 165 " distance=2.04 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 297 " distance=2.02 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 357 " distance=2.04 Simple disulfide: pdb=" SG CYS C 375 " - pdb=" SG CYS C 428 " distance=2.04 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 484 " distance=2.02 Simple disulfide: pdb=" SG CYS C 534 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 667 " distance=2.03 Simple disulfide: pdb=" SG CYS C 730 " - pdb=" SG CYS C 752 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 741 " distance=2.03 Simple disulfide: pdb=" SG CYS C 832 " - pdb=" SG CYS C 843 " distance=2.03 Simple disulfide: pdb=" SG CYS C1024 " - pdb=" SG CYS C1035 " distance=2.03 Simple disulfide: pdb=" SG CYS C1074 " - pdb=" SG CYS C1118 " distance=1.43 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 18 " " NAG A1302 " - " ASN A 612 " " NAG A1303 " - " ASN A 327 " " NAG A1304 " - " ASN A 339 " " NAG A1305 " - " ASN A 366 " " NAG A1306 " - " ASN A 793 " " NAG A1307 " - " ASN A1066 " " NAG A1308 " - " ASN A 31 " " NAG A1309 " - " ASN A 62 " " NAG A1310 " - " ASN A 653 " " NAG A1311 " - " ASN A 701 " " NAG A1312 " - " ASN A1090 " " NAG A1313 " - " ASN A1126 " " NAG B1301 " - " ASN B 327 " " NAG B1302 " - " ASN B 793 " " NAG B1303 " - " ASN B 653 " " NAG B1304 " - " ASN B 701 " " NAG B1305 " - " ASN B1090 " " NAG B1306 " - " ASN B1126 " " NAG B1307 " - " ASN B 18 " " NAG B1308 " - " ASN B1066 " " NAG B1309 " - " ASN B 339 " " NAG B1310 " - " ASN B 62 " " NAG B1311 " - " ASN B 31 " " NAG B1312 " - " ASN B 612 " " NAG B1313 " - " ASN B 366 " " NAG C1301 " - " ASN C 62 " " NAG C1302 " - " ASN C 612 " " NAG C1303 " - " ASN C 701 " " NAG C1304 " - " ASN C1090 " " NAG C1305 " - " ASN C 653 " " NAG C1306 " - " ASN C 18 " " NAG C1307 " - " ASN C1066 " " NAG C1308 " - " ASN C 793 " " NAG C1309 " - " ASN C 366 " " NAG C1310 " - " ASN C 327 " " NAG C1311 " - " ASN C 31 " " NAG C1312 " - " ASN C1126 " " NAG C1313 " - " ASN C 339 " " NAG D 1 " - " ASN A 233 " " NAG E 1 " - " ASN A 164 " " NAG F 1 " - " ASN A 122 " " NAG G 1 " - " ASN A 278 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN B 164 " " NAG J 1 " - " ASN B 122 " " NAG K 1 " - " ASN B 233 " " NAG L 1 " - " ASN B 278 " " NAG M 1 " - " ASN B 709 " " NAG N 1 " - " ASN C 278 " " NAG O 1 " - " ASN C 122 " " NAG P 1 " - " ASN C 233 " " NAG Q 1 " - " ASN C 709 " " NAG R 1 " - " ASN C 164 " Time building additional restraints: 11.15 Conformation dependent library (CDL) restraints added in 5.3 seconds 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6246 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 55 sheets defined 25.0% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 360 through 365 Processing helix chain 'A' and resid 379 through 385 removed outlier: 4.067A pdb=" N ASN A 384 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.614A pdb=" N ARG A 404 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 729 through 735 removed outlier: 3.887A pdb=" N TYR A 733 " --> pdb=" O ASP A 729 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 734 " --> pdb=" O CYS A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 750 through 774 removed outlier: 4.258A pdb=" N GLN A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 828 through 834 removed outlier: 3.557A pdb=" N CYS A 832 " --> pdb=" O GLN A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 848 Processing helix chain 'A' and resid 858 through 876 Processing helix chain 'A' and resid 878 through 882 removed outlier: 3.542A pdb=" N ALA A 882 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 900 Processing helix chain 'A' and resid 904 through 933 removed outlier: 4.434A pdb=" N LEU A 908 " --> pdb=" O THR A 904 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS A 913 " --> pdb=" O TYR A 909 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU A 914 " --> pdb=" O GLU A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 957 removed outlier: 3.699A pdb=" N ASP A 942 " --> pdb=" O GLY A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 960 No H-bonds generated for 'chain 'A' and resid 958 through 960' Processing helix chain 'A' and resid 968 through 974 Processing helix chain 'A' and resid 977 through 1025 removed outlier: 3.952A pdb=" N VAL A 983 " --> pdb=" O PRO A 979 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN A 984 " --> pdb=" O GLU A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1076 No H-bonds generated for 'chain 'A' and resid 1074 through 1076' Processing helix chain 'B' and resid 72 through 75 Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 360 through 365 Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 401 through 406 removed outlier: 4.726A pdb=" N ARG B 404 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 418 Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 621 through 625 Processing helix chain 'B' and resid 626 through 632 removed outlier: 4.180A pdb=" N TYR B 632 " --> pdb=" O THR B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 735 removed outlier: 3.729A pdb=" N TYR B 733 " --> pdb=" O ASP B 729 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 734 " --> pdb=" O CYS B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 750 through 775 removed outlier: 4.247A pdb=" N GLN B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 818 Processing helix chain 'B' and resid 828 through 834 Processing helix chain 'B' and resid 840 through 848 Processing helix chain 'B' and resid 858 through 876 Processing helix chain 'B' and resid 878 through 882 Processing helix chain 'B' and resid 889 through 900 removed outlier: 3.787A pdb=" N ALA B 895 " --> pdb=" O ALA B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 910 removed outlier: 4.913A pdb=" N TYR B 909 " --> pdb=" O ASN B 906 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU B 910 " --> pdb=" O VAL B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 933 removed outlier: 3.622A pdb=" N LEU B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER B 931 " --> pdb=" O GLN B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 957 removed outlier: 3.893A pdb=" N ASP B 942 " --> pdb=" O GLY B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 960 No H-bonds generated for 'chain 'B' and resid 958 through 960' Processing helix chain 'B' and resid 968 through 974 Processing helix chain 'B' and resid 977 through 1024 removed outlier: 4.033A pdb=" N VAL B 983 " --> pdb=" O PRO B 979 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN B 984 " --> pdb=" O GLU B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1076 No H-bonds generated for 'chain 'B' and resid 1074 through 1076' Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 360 through 367 removed outlier: 3.911A pdb=" N ASN C 366 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 385 removed outlier: 4.138A pdb=" N ASN C 384 " --> pdb=" O THR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 4.516A pdb=" N ARG C 404 " --> pdb=" O ASP C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'C' and resid 498 through 501 Processing helix chain 'C' and resid 612 through 614 No H-bonds generated for 'chain 'C' and resid 612 through 614' Processing helix chain 'C' and resid 615 through 621 Processing helix chain 'C' and resid 622 through 625 Processing helix chain 'C' and resid 626 through 632 removed outlier: 4.162A pdb=" N TYR C 632 " --> pdb=" O THR C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 735 Processing helix chain 'C' and resid 738 through 749 Processing helix chain 'C' and resid 750 through 774 removed outlier: 4.188A pdb=" N GLN C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 818 Processing helix chain 'C' and resid 828 through 834 removed outlier: 3.503A pdb=" N CYS C 832 " --> pdb=" O GLN C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 848 Processing helix chain 'C' and resid 858 through 876 Processing helix chain 'C' and resid 878 through 882 Processing helix chain 'C' and resid 889 through 900 Processing helix chain 'C' and resid 907 through 933 removed outlier: 6.240A pdb=" N LYS C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU C 914 " --> pdb=" O GLU C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 957 removed outlier: 3.671A pdb=" N ASP C 942 " --> pdb=" O GLY C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 960 No H-bonds generated for 'chain 'C' and resid 958 through 960' Processing helix chain 'C' and resid 968 through 974 Processing helix chain 'C' and resid 977 through 1025 removed outlier: 3.936A pdb=" N VAL C 983 " --> pdb=" O PRO C 979 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN C 984 " --> pdb=" O GLU C 980 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 7.740A pdb=" N ASN A 62 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N TYR A 265 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP A 186 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER A 204 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 37 removed outlier: 5.880A pdb=" N SER A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 56 removed outlier: 3.868A pdb=" N ASP A 283 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.974A pdb=" N THR A 242 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 101 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N VAL A 126 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N GLU A 168 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.282A pdb=" N ILE A 128 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N THR A 166 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL A 130 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ASN A 164 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASN A 132 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR A 162 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN A 134 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 323 Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.292A pdb=" N CYS A 357 " --> pdb=" O CYS A 521 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 390 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 390 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 448 through 450 Processing sheet with id=AB3, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB4, first strand: chain 'A' and resid 650 through 651 Processing sheet with id=AB5, first strand: chain 'A' and resid 703 through 705 removed outlier: 3.796A pdb=" N THR A1068 " --> pdb=" O SER A1089 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 709 through 710 Processing sheet with id=AB7, first strand: chain 'A' and resid 713 through 720 removed outlier: 6.798A pdb=" N VAL A1057 " --> pdb=" O LEU A1041 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 713 through 720 Processing sheet with id=AB9, first strand: chain 'A' and resid 726 through 728 Processing sheet with id=AC1, first strand: chain 'A' and resid 1078 through 1082 removed outlier: 4.456A pdb=" N ALA A1079 " --> pdb=" O SER A1115 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A1115 " --> pdb=" O ALA A1079 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 removed outlier: 7.653A pdb=" N ASN B 62 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TYR B 265 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP B 186 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER B 204 " --> pdb=" O PRO B 224 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 49 through 56 removed outlier: 3.902A pdb=" N ASP B 283 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.667A pdb=" N ARG B 245 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR B 144 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.965A pdb=" N THR B 242 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL B 101 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 11.275A pdb=" N ILE B 128 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N THR B 166 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL B 130 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASN B 164 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASN B 132 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR B 162 " --> pdb=" O ASN B 132 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN B 134 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 307 through 310 Processing sheet with id=AC8, first strand: chain 'B' and resid 321 through 323 Processing sheet with id=AC9, first strand: chain 'B' and resid 344 through 345 removed outlier: 7.145A pdb=" N ALA B 344 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N ARG B 399 " --> pdb=" O ALA B 344 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 344 through 345 removed outlier: 7.145A pdb=" N ALA B 344 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N ARG B 399 " --> pdb=" O ALA B 344 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 357 through 358 removed outlier: 6.382A pdb=" N CYS B 357 " --> pdb=" O CYS B 521 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 448 through 450 Processing sheet with id=AD4, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AD5, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AD6, first strand: chain 'B' and resid 703 through 705 removed outlier: 3.934A pdb=" N THR B1068 " --> pdb=" O SER B1089 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 713 through 720 Processing sheet with id=AD8, first strand: chain 'B' and resid 726 through 728 Processing sheet with id=AD9, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AE1, first strand: chain 'B' and resid 1078 through 1082 removed outlier: 4.385A pdb=" N ALA B1079 " --> pdb=" O SER B1115 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AE3, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.534A pdb=" N ASN C 62 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TYR C 265 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP C 186 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N SER C 204 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 49 through 56 removed outlier: 3.862A pdb=" N ASP C 283 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.998A pdb=" N PHE C 237 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 13.078A pdb=" N TYR C 137 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 10.273A pdb=" N THR C 239 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU C 241 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLN C 134 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL C 158 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.979A pdb=" N THR C 242 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL C 101 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL C 126 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 307 through 310 Processing sheet with id=AE8, first strand: chain 'C' and resid 321 through 323 removed outlier: 5.610A pdb=" N ASP C 570 " --> pdb=" O ILE C 583 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.399A pdb=" N CYS C 357 " --> pdb=" O CYS C 521 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 390 through 392 Processing sheet with id=AF2, first strand: chain 'C' and resid 390 through 392 Processing sheet with id=AF3, first strand: chain 'C' and resid 448 through 450 Processing sheet with id=AF4, first strand: chain 'C' and resid 469 through 470 Processing sheet with id=AF5, first strand: chain 'C' and resid 650 through 651 Processing sheet with id=AF6, first strand: chain 'C' and resid 703 through 705 removed outlier: 3.884A pdb=" N THR C1068 " --> pdb=" O SER C1089 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 713 through 720 removed outlier: 6.735A pdb=" N VAL C1057 " --> pdb=" O LEU C1041 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 713 through 720 Processing sheet with id=AF9, first strand: chain 'C' and resid 726 through 728 Processing sheet with id=AG1, first strand: chain 'C' and resid 1073 through 1075 removed outlier: 4.787A pdb=" N ALA C1079 " --> pdb=" O SER C1115 " (cutoff:3.500A) 1053 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.96 Time building geometry restraints manager: 11.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 8585 1.35 - 1.48: 7288 1.48 - 1.61: 11577 1.61 - 1.74: 0 1.74 - 1.87: 156 Bond restraints: 27606 Sorted by residual: bond pdb=" N VAL B1120 " pdb=" CA VAL B1120 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.19e-02 7.06e+03 1.10e+01 bond pdb=" N VAL A1120 " pdb=" CA VAL A1120 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N ILE C1124 " pdb=" CA ILE C1124 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.14e-02 7.69e+03 9.86e+00 bond pdb=" N ILE A1124 " pdb=" CA ILE A1124 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.46e+00 bond pdb=" C SER B1115 " pdb=" N GLY B1116 " ideal model delta sigma weight residual 1.331 1.287 0.044 1.46e-02 4.69e+03 8.93e+00 ... (remaining 27601 not shown) Histogram of bond angle deviations from ideal: 95.39 - 103.13: 178 103.13 - 110.86: 9734 110.86 - 118.60: 12110 118.60 - 126.33: 15269 126.33 - 134.07: 299 Bond angle restraints: 37590 Sorted by residual: angle pdb=" N VAL A1120 " pdb=" CA VAL A1120 " pdb=" C VAL A1120 " ideal model delta sigma weight residual 111.90 95.39 16.51 8.10e-01 1.52e+00 4.15e+02 angle pdb=" N VAL B1120 " pdb=" CA VAL B1120 " pdb=" C VAL B1120 " ideal model delta sigma weight residual 111.90 96.45 15.45 8.10e-01 1.52e+00 3.64e+02 angle pdb=" N ILE C1122 " pdb=" CA ILE C1122 " pdb=" C ILE C1122 " ideal model delta sigma weight residual 110.53 121.58 -11.05 9.40e-01 1.13e+00 1.38e+02 angle pdb=" C SER B1115 " pdb=" N GLY B1116 " pdb=" CA GLY B1116 " ideal model delta sigma weight residual 121.41 104.99 16.42 1.96e+00 2.60e-01 7.02e+01 angle pdb=" C ILE C1122 " pdb=" CA ILE C1122 " pdb=" CB ILE C1122 " ideal model delta sigma weight residual 112.02 101.55 10.47 1.31e+00 5.83e-01 6.39e+01 ... (remaining 37585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.28: 16002 20.28 - 40.56: 1066 40.56 - 60.84: 189 60.84 - 81.11: 34 81.11 - 101.39: 28 Dihedral angle restraints: 17319 sinusoidal: 7572 harmonic: 9747 Sorted by residual: dihedral pdb=" CB CYS A1074 " pdb=" SG CYS A1074 " pdb=" SG CYS A1118 " pdb=" CB CYS A1118 " ideal model delta sinusoidal sigma weight residual 93.00 15.03 77.97 1 1.00e+01 1.00e-02 7.60e+01 dihedral pdb=" CA CYS C 375 " pdb=" C CYS C 375 " pdb=" N TYR C 376 " pdb=" CA TYR C 376 " ideal model delta harmonic sigma weight residual 180.00 -138.16 -41.84 0 5.00e+00 4.00e-02 7.00e+01 dihedral pdb=" CB CYS A 375 " pdb=" SG CYS A 375 " pdb=" SG CYS A 428 " pdb=" CB CYS A 428 " ideal model delta sinusoidal sigma weight residual 93.00 34.08 58.92 1 1.00e+01 1.00e-02 4.64e+01 ... (remaining 17316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 4413 0.157 - 0.313: 28 0.313 - 0.470: 8 0.470 - 0.626: 2 0.626 - 0.783: 1 Chirality restraints: 4452 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.78e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.50e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.23e+01 ... (remaining 4449 not shown) Planarity restraints: 4836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " 0.351 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG B1304 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " 0.093 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " -0.539 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " 0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1303 " 0.316 2.00e-02 2.50e+03 2.67e-01 8.89e+02 pdb=" C7 NAG C1303 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C1303 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG C1303 " -0.461 2.00e-02 2.50e+03 pdb=" O7 NAG C1303 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1313 " -0.243 2.00e-02 2.50e+03 2.03e-01 5.15e+02 pdb=" C7 NAG A1313 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG A1313 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG A1313 " 0.338 2.00e-02 2.50e+03 pdb=" O7 NAG A1313 " 0.009 2.00e-02 2.50e+03 ... (remaining 4833 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 175 2.47 - 3.08: 19217 3.08 - 3.69: 40687 3.69 - 4.29: 64031 4.29 - 4.90: 104256 Nonbonded interactions: 228366 Sorted by model distance: nonbonded pdb=" OD1 ASN A1126 " pdb=" N ASN A1127 " model vdw 1.868 2.520 nonbonded pdb=" OD1 ASN C1126 " pdb=" N ASN C1127 " model vdw 1.868 2.520 nonbonded pdb=" OD1 ASN B1126 " pdb=" N ASN B1127 " model vdw 1.869 2.520 nonbonded pdb=" O CYS C1074 " pdb=" CB ASN C1126 " model vdw 2.031 3.440 nonbonded pdb=" OG1 THR C 549 " pdb=" OD1 ASP C 582 " model vdw 2.072 2.440 ... (remaining 228361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.160 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 79.580 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27606 Z= 0.292 Angle : 0.713 16.510 37590 Z= 0.418 Chirality : 0.055 0.783 4452 Planarity : 0.008 0.304 4782 Dihedral : 14.070 101.393 10941 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -1.71 (0.14), residues: 3339 helix: -0.38 (0.18), residues: 741 sheet: -0.02 (0.21), residues: 636 loop : -1.90 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C1094 HIS 0.005 0.001 HIS B1040 PHE 0.038 0.002 PHE B 343 TYR 0.022 0.002 TYR B 262 ARG 0.005 0.000 ARG C1099 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 3.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.0629 (mmp) cc_final: -0.0555 (mpp) REVERT: A 257 PHE cc_start: 0.7063 (m-80) cc_final: 0.6427 (m-80) REVERT: A 765 GLU cc_start: 0.7120 (tp30) cc_final: 0.6799 (tp30) REVERT: A 1114 VAL cc_start: 0.7195 (p) cc_final: 0.6975 (p) REVERT: B 765 GLU cc_start: 0.7033 (tp30) cc_final: 0.6804 (tp30) REVERT: B 878 TRP cc_start: 0.7503 (p90) cc_final: 0.6512 (p90) outliers start: 0 outliers final: 1 residues processed: 364 average time/residue: 1.1235 time to fit residues: 491.4415 Evaluate side-chains 257 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 256 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 436 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 134 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 302 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 GLN A 609 GLN ** A 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1127 ASN B 115 GLN B1002 GLN B1127 ASN C 609 GLN C 754 GLN C 771 GLN C 776 GLN C1100 ASN C1127 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 27606 Z= 0.362 Angle : 0.681 14.095 37590 Z= 0.360 Chirality : 0.052 0.657 4452 Planarity : 0.005 0.047 4782 Dihedral : 8.422 81.824 5069 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.13 % Favored : 90.84 % Rotamer: Outliers : 2.11 % Allowed : 8.60 % Favored : 89.29 % 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: -1.66 (0.14), residues: 3339 helix: -0.13 (0.19), residues: 723 sheet: -0.20 (0.21), residues: 657 loop : -1.88 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1094 HIS 0.007 0.001 HIS A 34 PHE 0.034 0.002 PHE B 343 TYR 0.020 0.002 TYR C 419 ARG 0.005 0.001 ARG C1099 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 275 time to evaluate : 3.143 Fit side-chains revert: symmetry clash REVERT: A 175 MET cc_start: 0.0646 (mmp) cc_final: -0.0510 (mpp) REVERT: A 257 PHE cc_start: 0.7039 (m-80) cc_final: 0.6419 (m-80) REVERT: A 1002 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7390 (mp-120) REVERT: B 262 TYR cc_start: 0.6747 (OUTLIER) cc_final: 0.6281 (m-80) REVERT: B 751 PHE cc_start: 0.6841 (OUTLIER) cc_final: 0.6524 (m-80) REVERT: B 831 ASP cc_start: 0.6824 (m-30) cc_final: 0.6585 (m-30) REVERT: C 139 PRO cc_start: 0.7600 (Cg_endo) cc_final: 0.7381 (Cg_exo) REVERT: C 204 SER cc_start: 0.8254 (p) cc_final: 0.7950 (p) REVERT: C 740 GLU cc_start: 0.6477 (pm20) cc_final: 0.6089 (pm20) outliers start: 61 outliers final: 32 residues processed: 307 average time/residue: 1.1298 time to fit residues: 420.0703 Evaluate side-chains 290 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 255 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1100 ASN Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 908 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 302 optimal weight: 4.9990 chunk 327 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 300 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 214 ASN B 918 GLN B1002 GLN C 754 GLN C 769 ASN C 771 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 27606 Z= 0.295 Angle : 0.637 11.184 37590 Z= 0.336 Chirality : 0.050 0.651 4452 Planarity : 0.004 0.045 4782 Dihedral : 7.974 81.364 5069 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.76 % Allowed : 11.09 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3339 helix: 0.09 (0.19), residues: 723 sheet: -0.24 (0.21), residues: 654 loop : -1.90 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1094 HIS 0.006 0.001 HIS A 34 PHE 0.029 0.002 PHE B 809 TYR 0.017 0.002 TYR A 419 ARG 0.004 0.000 ARG C1099 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 272 time to evaluate : 3.023 Fit side-chains revert: symmetry clash REVERT: A 111 ASP cc_start: 0.6901 (p0) cc_final: 0.6696 (p0) REVERT: A 175 MET cc_start: 0.0515 (mmp) cc_final: -0.0578 (mpp) REVERT: A 257 PHE cc_start: 0.6944 (m-80) cc_final: 0.6453 (m-80) REVERT: A 740 GLU cc_start: 0.6836 (pm20) cc_final: 0.6612 (pm20) REVERT: B 262 TYR cc_start: 0.6775 (OUTLIER) cc_final: 0.6423 (m-80) REVERT: B 731 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8166 (p) REVERT: B 751 PHE cc_start: 0.6855 (OUTLIER) cc_final: 0.6485 (m-80) REVERT: B 878 TRP cc_start: 0.7552 (p90) cc_final: 0.6586 (p90) REVERT: C 85 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: C 139 PRO cc_start: 0.7561 (Cg_endo) cc_final: 0.7209 (Cg_exo) REVERT: C 204 SER cc_start: 0.8250 (p) cc_final: 0.7905 (p) REVERT: C 740 GLU cc_start: 0.6523 (pm20) cc_final: 0.6303 (pm20) REVERT: C 768 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7550 (tttt) REVERT: C 1002 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.6940 (mp10) outliers start: 80 outliers final: 36 residues processed: 318 average time/residue: 1.1473 time to fit residues: 439.2443 Evaluate side-chains 289 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 247 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1100 ASN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 768 LYS Chi-restraints excluded: chain C residue 861 MET Chi-restraints excluded: chain C residue 1002 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 299 optimal weight: 0.8980 chunk 227 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 304 optimal weight: 10.0000 chunk 321 optimal weight: 1.9990 chunk 158 optimal weight: 0.3980 chunk 288 optimal weight: 0.0970 chunk 86 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 ASN B1002 GLN ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN C 796 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 27606 Z= 0.272 Angle : 0.625 12.618 37590 Z= 0.328 Chirality : 0.050 0.615 4452 Planarity : 0.004 0.045 4782 Dihedral : 7.743 80.918 5069 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.87 % Allowed : 12.95 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3339 helix: 0.23 (0.19), residues: 723 sheet: -0.29 (0.21), residues: 684 loop : -1.86 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C1094 HIS 0.004 0.001 HIS A 34 PHE 0.032 0.002 PHE B 809 TYR 0.015 0.002 TYR A 419 ARG 0.003 0.000 ARG C1099 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 270 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.6885 (p0) cc_final: 0.6683 (p0) REVERT: A 175 MET cc_start: 0.0522 (mmp) cc_final: -0.0567 (mpp) REVERT: A 257 PHE cc_start: 0.6977 (m-80) cc_final: 0.6455 (m-80) REVERT: A 740 GLU cc_start: 0.6849 (pm20) cc_final: 0.6598 (pm20) REVERT: B 731 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8208 (p) REVERT: B 751 PHE cc_start: 0.6874 (OUTLIER) cc_final: 0.6532 (m-80) REVERT: B 768 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7836 (ttpt) REVERT: B 878 TRP cc_start: 0.7574 (p90) cc_final: 0.6545 (p90) REVERT: B 1042 MET cc_start: 0.7809 (ptm) cc_final: 0.7583 (ptp) REVERT: C 85 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7206 (m-30) REVERT: C 139 PRO cc_start: 0.7595 (Cg_endo) cc_final: 0.7166 (Cg_exo) REVERT: C 768 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7536 (tttt) REVERT: C 1002 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.6790 (mp10) outliers start: 83 outliers final: 42 residues processed: 320 average time/residue: 1.1346 time to fit residues: 436.5479 Evaluate side-chains 300 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 252 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1100 ASN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 768 LYS Chi-restraints excluded: chain C residue 1002 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 268 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 239 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 274 optimal weight: 0.6980 chunk 222 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 288 optimal weight: 0.0470 chunk 81 optimal weight: 10.0000 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN ** A 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 754 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 27606 Z= 0.245 Angle : 0.607 10.244 37590 Z= 0.320 Chirality : 0.049 0.583 4452 Planarity : 0.004 0.053 4782 Dihedral : 7.478 80.717 5069 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.83 % Allowed : 14.06 % Favored : 83.11 % 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: -1.46 (0.14), residues: 3339 helix: 0.37 (0.20), residues: 723 sheet: -0.23 (0.21), residues: 654 loop : -1.83 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1094 HIS 0.003 0.001 HIS A 34 PHE 0.022 0.002 PHE B 809 TYR 0.016 0.001 TYR A1059 ARG 0.006 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 280 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.6817 (p0) cc_final: 0.6616 (p0) REVERT: A 175 MET cc_start: 0.0972 (mmp) cc_final: -0.0356 (mpp) REVERT: A 249 MET cc_start: 0.1080 (ppp) cc_final: 0.0079 (ptp) REVERT: A 257 PHE cc_start: 0.6948 (m-80) cc_final: 0.6434 (m-80) REVERT: A 740 GLU cc_start: 0.6861 (pm20) cc_final: 0.6628 (pm20) REVERT: A 1002 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: B 731 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8205 (p) REVERT: B 751 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.6546 (m-80) REVERT: B 878 TRP cc_start: 0.7531 (p90) cc_final: 0.6523 (p90) REVERT: B 1042 MET cc_start: 0.7772 (ptm) cc_final: 0.7537 (ptp) REVERT: C 85 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7194 (m-30) REVERT: C 139 PRO cc_start: 0.7586 (Cg_endo) cc_final: 0.7155 (Cg_exo) REVERT: C 204 SER cc_start: 0.8189 (p) cc_final: 0.7837 (p) REVERT: C 751 PHE cc_start: 0.6333 (OUTLIER) cc_final: 0.6051 (m-80) REVERT: C 768 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7573 (tttt) REVERT: C 1002 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.6769 (mp10) outliers start: 82 outliers final: 49 residues processed: 327 average time/residue: 1.1023 time to fit residues: 437.6803 Evaluate side-chains 303 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 247 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 861 MET Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1098 GLN Chi-restraints excluded: chain A residue 1100 ASN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 751 PHE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 768 LYS Chi-restraints excluded: chain C residue 861 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1100 ASN Chi-restraints excluded: chain C residue 1124 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 108 optimal weight: 4.9990 chunk 289 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 322 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1100 ASN B 214 ASN B1002 GLN C 754 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 27606 Z= 0.506 Angle : 0.775 18.861 37590 Z= 0.405 Chirality : 0.056 0.552 4452 Planarity : 0.005 0.054 4782 Dihedral : 8.181 81.961 5069 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.55 % Favored : 90.39 % Rotamer: Outliers : 3.45 % Allowed : 15.13 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.14), residues: 3339 helix: -0.20 (0.19), residues: 729 sheet: -0.51 (0.20), residues: 723 loop : -1.94 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A1094 HIS 0.009 0.002 HIS A 34 PHE 0.033 0.003 PHE B 794 TYR 0.026 0.003 TYR B 419 ARG 0.005 0.001 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 258 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.0665 (mmp) cc_final: -0.0581 (mpp) REVERT: A 249 MET cc_start: 0.1169 (ppp) cc_final: -0.0114 (ptp) REVERT: A 257 PHE cc_start: 0.6943 (m-80) cc_final: 0.6413 (m-80) REVERT: A 1002 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7963 (mp10) REVERT: B 204 SER cc_start: 0.8031 (p) cc_final: 0.7767 (p) REVERT: B 751 PHE cc_start: 0.6805 (OUTLIER) cc_final: 0.6429 (m-80) REVERT: B 768 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8283 (ttpt) REVERT: B 772 GLU cc_start: 0.7079 (pt0) cc_final: 0.6840 (pt0) REVERT: B 1042 MET cc_start: 0.7902 (ptm) cc_final: 0.7700 (ptp) REVERT: B 1106 ILE cc_start: 0.7566 (mm) cc_final: 0.7243 (tp) REVERT: C 139 PRO cc_start: 0.7581 (Cg_endo) cc_final: 0.7116 (Cg_exo) REVERT: C 204 SER cc_start: 0.8259 (p) cc_final: 0.7956 (p) REVERT: C 751 PHE cc_start: 0.6333 (OUTLIER) cc_final: 0.6081 (m-80) REVERT: C 771 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6887 (tp40) REVERT: C 1002 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.6887 (mp10) outliers start: 100 outliers final: 62 residues processed: 328 average time/residue: 1.1107 time to fit residues: 440.8108 Evaluate side-chains 304 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 236 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 861 MET Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1098 GLN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 831 ASP Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 642 ARG Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 751 PHE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 771 GLN Chi-restraints excluded: chain C residue 796 GLN Chi-restraints excluded: chain C residue 861 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1100 ASN Chi-restraints excluded: chain C residue 1125 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 310 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 183 optimal weight: 0.7980 chunk 235 optimal weight: 20.0000 chunk 182 optimal weight: 0.7980 chunk 271 optimal weight: 0.6980 chunk 179 optimal weight: 0.8980 chunk 320 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN ** A 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B1002 GLN C 893 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27606 Z= 0.212 Angle : 0.613 13.290 37590 Z= 0.322 Chirality : 0.048 0.536 4452 Planarity : 0.004 0.046 4782 Dihedral : 7.543 81.524 5069 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.06 % Favored : 91.91 % Rotamer: Outliers : 2.38 % Allowed : 16.86 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3339 helix: 0.20 (0.19), residues: 747 sheet: -0.47 (0.21), residues: 681 loop : -1.81 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1094 HIS 0.004 0.001 HIS B1080 PHE 0.016 0.001 PHE A 794 TYR 0.032 0.001 TYR C 896 ARG 0.005 0.000 ARG C1083 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 261 time to evaluate : 3.278 Fit side-chains REVERT: A 175 MET cc_start: 0.1068 (mmp) cc_final: -0.0329 (mpp) REVERT: A 249 MET cc_start: 0.0978 (ppp) cc_final: -0.0161 (ptt) REVERT: A 257 PHE cc_start: 0.6940 (m-80) cc_final: 0.6431 (m-80) REVERT: A 740 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6660 (pm20) REVERT: A 1002 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: B 204 SER cc_start: 0.8219 (p) cc_final: 0.7905 (p) REVERT: B 751 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.6386 (m-80) REVERT: B 878 TRP cc_start: 0.7568 (p90) cc_final: 0.6586 (p90) REVERT: B 1042 MET cc_start: 0.7760 (ptm) cc_final: 0.7499 (ptp) REVERT: C 139 PRO cc_start: 0.7493 (Cg_endo) cc_final: 0.7044 (Cg_exo) REVERT: C 204 SER cc_start: 0.8177 (p) cc_final: 0.7816 (p) REVERT: C 751 PHE cc_start: 0.6166 (OUTLIER) cc_final: 0.5914 (m-80) REVERT: C 768 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7262 (tttt) REVERT: C 1002 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.6779 (mp10) outliers start: 69 outliers final: 39 residues processed: 307 average time/residue: 1.0996 time to fit residues: 409.7099 Evaluate side-chains 287 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 242 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 642 ARG Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 751 PHE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 768 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1047 SER Chi-restraints excluded: chain C residue 1100 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 198 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 96 optimal weight: 0.0170 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 204 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B1002 GLN B1105 GLN C 754 GLN C 771 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27606 Z= 0.258 Angle : 0.625 14.530 37590 Z= 0.328 Chirality : 0.049 0.511 4452 Planarity : 0.004 0.045 4782 Dihedral : 7.483 80.608 5069 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.66 % Favored : 91.31 % Rotamer: Outliers : 2.87 % Allowed : 16.68 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3339 helix: 0.35 (0.19), residues: 723 sheet: -0.36 (0.20), residues: 720 loop : -1.82 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1094 HIS 0.003 0.001 HIS A1040 PHE 0.021 0.002 PHE B 794 TYR 0.014 0.002 TYR C 419 ARG 0.003 0.000 ARG C 839 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 247 time to evaluate : 3.328 Fit side-chains revert: symmetry clash REVERT: A 175 MET cc_start: 0.1176 (mmp) cc_final: -0.0260 (mpp) REVERT: A 249 MET cc_start: 0.0772 (ppp) cc_final: 0.0153 (ptt) REVERT: A 257 PHE cc_start: 0.6925 (m-80) cc_final: 0.6598 (m-80) REVERT: A 740 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6653 (pm20) REVERT: A 1002 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7672 (mp10) REVERT: B 751 PHE cc_start: 0.6792 (OUTLIER) cc_final: 0.6378 (m-80) REVERT: B 768 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8210 (tttm) REVERT: B 878 TRP cc_start: 0.7585 (p90) cc_final: 0.6565 (p90) REVERT: B 1042 MET cc_start: 0.7791 (ptm) cc_final: 0.7518 (ptp) REVERT: C 80 ASP cc_start: 0.6842 (OUTLIER) cc_final: 0.6271 (p0) REVERT: C 139 PRO cc_start: 0.7504 (Cg_endo) cc_final: 0.7050 (Cg_exo) REVERT: C 204 SER cc_start: 0.8214 (p) cc_final: 0.7855 (p) REVERT: C 751 PHE cc_start: 0.6184 (OUTLIER) cc_final: 0.5932 (m-80) REVERT: C 892 MET cc_start: 0.6180 (ptm) cc_final: 0.5911 (ptp) REVERT: C 1002 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.6795 (mp10) outliers start: 83 outliers final: 54 residues processed: 307 average time/residue: 1.1481 time to fit residues: 429.1855 Evaluate side-chains 298 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 237 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 831 ASP Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1112 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 642 ARG Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 751 PHE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 861 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1047 SER Chi-restraints excluded: chain C residue 1100 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 291 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 280 optimal weight: 0.5980 chunk 299 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 chunk 130 optimal weight: 0.3980 chunk 234 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 214 ASN B1002 GLN C 115 GLN C 754 GLN ** C 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27606 Z= 0.201 Angle : 0.598 15.804 37590 Z= 0.314 Chirality : 0.047 0.489 4452 Planarity : 0.004 0.048 4782 Dihedral : 7.197 80.051 5069 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.25 % Allowed : 17.65 % Favored : 80.10 % 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: -1.34 (0.14), residues: 3339 helix: 0.54 (0.20), residues: 723 sheet: -0.08 (0.21), residues: 672 loop : -1.83 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1094 HIS 0.003 0.001 HIS B1040 PHE 0.016 0.001 PHE A 794 TYR 0.013 0.001 TYR B 261 ARG 0.003 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 262 time to evaluate : 3.276 Fit side-chains revert: symmetry clash REVERT: A 175 MET cc_start: 0.0996 (mmp) cc_final: -0.0086 (mpp) REVERT: A 249 MET cc_start: 0.0922 (ppp) cc_final: 0.0403 (ptt) REVERT: A 257 PHE cc_start: 0.6924 (m-80) cc_final: 0.6625 (m-80) REVERT: A 529 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7106 (tt) REVERT: A 1002 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7580 (mp10) REVERT: B 204 SER cc_start: 0.8155 (p) cc_final: 0.7839 (p) REVERT: B 751 PHE cc_start: 0.6733 (OUTLIER) cc_final: 0.6377 (m-80) REVERT: B 768 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8233 (tttm) REVERT: B 878 TRP cc_start: 0.7566 (p90) cc_final: 0.6574 (p90) REVERT: B 1042 MET cc_start: 0.7768 (ptm) cc_final: 0.7494 (ptp) REVERT: C 139 PRO cc_start: 0.7446 (Cg_endo) cc_final: 0.7007 (Cg_exo) REVERT: C 204 SER cc_start: 0.8165 (p) cc_final: 0.7787 (p) REVERT: C 244 HIS cc_start: 0.5828 (t-90) cc_final: 0.5536 (t-90) REVERT: C 751 PHE cc_start: 0.6163 (OUTLIER) cc_final: 0.5922 (m-80) outliers start: 65 outliers final: 46 residues processed: 310 average time/residue: 1.0557 time to fit residues: 399.7491 Evaluate side-chains 301 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 250 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 751 PHE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 861 MET Chi-restraints excluded: chain C residue 1047 SER Chi-restraints excluded: chain C residue 1100 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 196 optimal weight: 4.9990 chunk 316 optimal weight: 0.0370 chunk 193 optimal weight: 9.9990 chunk 150 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 331 optimal weight: 0.8980 chunk 305 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 27 optimal weight: 0.0870 chunk 204 optimal weight: 0.9990 chunk 161 optimal weight: 0.0170 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 864 GLN ** A 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B1002 GLN C 115 GLN C 754 GLN C 769 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27606 Z= 0.171 Angle : 0.583 14.574 37590 Z= 0.306 Chirality : 0.047 0.475 4452 Planarity : 0.004 0.046 4782 Dihedral : 6.919 79.063 5069 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 1.55 % Allowed : 18.45 % Favored : 80.00 % 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: -1.21 (0.14), residues: 3339 helix: 0.65 (0.20), residues: 741 sheet: -0.26 (0.20), residues: 708 loop : -1.68 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1094 HIS 0.004 0.001 HIS B1040 PHE 0.014 0.001 PHE B 558 TYR 0.018 0.001 TYR C 909 ARG 0.004 0.000 ARG B 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 271 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.0701 (mmp) cc_final: -0.0394 (mpp) REVERT: A 249 MET cc_start: 0.1089 (ppp) cc_final: 0.0560 (ptt) REVERT: A 257 PHE cc_start: 0.6979 (m-80) cc_final: 0.6644 (m-80) REVERT: A 529 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7044 (tt) REVERT: A 723 MET cc_start: 0.8705 (ptt) cc_final: 0.8402 (ptt) REVERT: A 727 SER cc_start: 0.7905 (OUTLIER) cc_final: 0.7693 (t) REVERT: A 1002 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7806 (mt0) REVERT: B 731 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8247 (p) REVERT: B 878 TRP cc_start: 0.7549 (p90) cc_final: 0.6527 (p90) REVERT: B 1042 MET cc_start: 0.7730 (ptm) cc_final: 0.7434 (ptp) REVERT: C 115 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7314 (mt0) REVERT: C 139 PRO cc_start: 0.7418 (Cg_endo) cc_final: 0.6990 (Cg_exo) REVERT: C 244 HIS cc_start: 0.5768 (t-90) cc_final: 0.5333 (t70) REVERT: C 751 PHE cc_start: 0.6233 (OUTLIER) cc_final: 0.5974 (m-80) REVERT: C 1002 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.6816 (mp10) outliers start: 45 outliers final: 28 residues processed: 303 average time/residue: 1.0932 time to fit residues: 402.9108 Evaluate side-chains 287 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 252 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 751 PHE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 1002 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 209 optimal weight: 0.9990 chunk 281 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 243 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 73 optimal weight: 0.4980 chunk 264 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 864 GLN ** A 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 HIS B 214 ASN B 769 ASN B1002 GLN C 754 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.175504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.149743 restraints weight = 36271.219| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.13 r_work: 0.3664 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27606 Z= 0.188 Angle : 0.585 14.408 37590 Z= 0.307 Chirality : 0.047 0.469 4452 Planarity : 0.004 0.045 4782 Dihedral : 6.800 78.313 5069 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 1.62 % Allowed : 18.72 % Favored : 79.65 % 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: -1.17 (0.15), residues: 3339 helix: 0.71 (0.20), residues: 741 sheet: -0.32 (0.20), residues: 738 loop : -1.64 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A1094 HIS 0.003 0.001 HIS B1040 PHE 0.020 0.001 PHE B1067 TYR 0.021 0.001 TYR C 419 ARG 0.003 0.000 ARG B 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8305.28 seconds wall clock time: 149 minutes 57.80 seconds (8997.80 seconds total)