Starting phenix.real_space_refine on Tue Feb 20 01:51:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnr_33324/02_2024/7xnr_33324.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnr_33324/02_2024/7xnr_33324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnr_33324/02_2024/7xnr_33324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnr_33324/02_2024/7xnr_33324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnr_33324/02_2024/7xnr_33324.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnr_33324/02_2024/7xnr_33324.pdb" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 16860 2.51 5 N 4329 2.21 5 O 5154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C PHE 1062": "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: 26460 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8554 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8554 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8554 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 13.38, per 1000 atoms: 0.51 Number of scatterers: 26460 At special positions: 0 Unit cell: (156.22, 149.8, 184.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 5154 8.00 N 4329 7.00 C 16860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 61 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 122 " " NAG A1307 " - " ASN A 234 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 331 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 234 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 331 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 234 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 331 " " NAG D 1 " - " ASN A 709 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 709 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 709 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Time building additional restraints: 9.64 Conformation dependent library (CDL) restraints added in 4.7 seconds 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6144 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 51 sheets defined 24.5% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.998A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.567A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.186A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.405A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 removed outlier: 4.058A pdb=" N ALA A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 618 through 624 removed outlier: 4.376A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.737A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.697A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 772 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.581A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 removed outlier: 3.987A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 854' Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.532A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.363A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.769A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 941 removed outlier: 6.692A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 965 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.931A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1150 removed outlier: 3.827A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A1150 " --> pdb=" O ASP A1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.868A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.829A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.549A pdb=" N PHE B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 4.313A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.276A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 618 through 624 removed outlier: 4.134A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.858A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.531A pdb=" N THR B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.554A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.769A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 850 through 854' Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.605A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 914 No H-bonds generated for 'chain 'B' and resid 912 through 914' Processing helix chain 'B' and resid 915 through 941 removed outlier: 5.902A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 965 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.996A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG B1000 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1150 removed outlier: 3.936A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B1150 " --> pdb=" O ASP B1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.991A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.706A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.527A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.445A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 502 through 505 removed outlier: 3.613A pdb=" N HIS C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 505' Processing helix chain 'C' and resid 618 through 624 removed outlier: 4.492A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.803A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.703A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 772 " --> pdb=" O THR C 768 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.516A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 854 removed outlier: 3.527A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 850 through 854' Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.787A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 941 removed outlier: 6.786A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 965 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.900A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C1000 " --> pdb=" O LEU C 996 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1148 removed outlier: 4.027A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.541A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.788A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 64 removed outlier: 3.721A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 131 removed outlier: 3.606A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.131A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.888A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 542 through 543 removed outlier: 3.809A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.789A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.519A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.588A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 714 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 719 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 719 removed outlier: 3.666A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.671A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 788 removed outlier: 3.546A pdb=" N ILE A 788 " --> pdb=" O ALA B 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.751A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.972A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 126 through 131 removed outlier: 3.789A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.234A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 326 removed outlier: 7.769A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.583A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.628A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.634A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 712 through 719 removed outlier: 6.402A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 712 through 719 removed outlier: 6.402A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 787 through 788 removed outlier: 3.616A pdb=" N ILE B 788 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.950A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 63 through 64 removed outlier: 3.612A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 126 through 131 removed outlier: 6.127A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.286A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 325 removed outlier: 7.555A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.550A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 542 through 543 removed outlier: 3.871A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 551 through 554 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.294A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 712 through 728 removed outlier: 5.956A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.601A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'C' and resid 1094 through 1096 874 hydrogen bonds defined for protein. 2319 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.69 Time building geometry restraints manager: 10.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6717 1.33 - 1.45: 5919 1.45 - 1.58: 14303 1.58 - 1.70: 1 1.70 - 1.82: 150 Bond restraints: 27090 Sorted by residual: bond pdb=" CB PRO B 491 " pdb=" CG PRO B 491 " ideal model delta sigma weight residual 1.492 1.626 -0.134 5.00e-02 4.00e+02 7.19e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.89e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.38e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" CG PRO B 491 " pdb=" CD PRO B 491 " ideal model delta sigma weight residual 1.503 1.445 0.058 3.40e-02 8.65e+02 2.88e+00 ... (remaining 27085 not shown) Histogram of bond angle deviations from ideal: 96.71 - 104.17: 416 104.17 - 111.62: 12676 111.62 - 119.08: 9057 119.08 - 126.54: 14423 126.54 - 134.00: 319 Bond angle restraints: 36891 Sorted by residual: angle pdb=" CA PRO B 491 " pdb=" N PRO B 491 " pdb=" CD PRO B 491 " ideal model delta sigma weight residual 112.00 102.73 9.27 1.40e+00 5.10e-01 4.39e+01 angle pdb=" N PRO B 491 " pdb=" CD PRO B 491 " pdb=" CG PRO B 491 " ideal model delta sigma weight residual 103.20 96.71 6.49 1.50e+00 4.44e-01 1.87e+01 angle pdb=" N GLY B 757 " pdb=" CA GLY B 757 " pdb=" C GLY B 757 " ideal model delta sigma weight residual 110.29 115.02 -4.73 1.28e+00 6.10e-01 1.36e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 121.54 128.12 -6.58 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C ALA B 570 " pdb=" N ASP B 571 " pdb=" CA ASP B 571 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 ... (remaining 36886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.72: 15850 23.72 - 47.45: 795 47.45 - 71.17: 111 71.17 - 94.90: 47 94.90 - 118.62: 36 Dihedral angle restraints: 16839 sinusoidal: 7272 harmonic: 9567 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 2.92 -88.92 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 6.74 86.26 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 10.92 82.08 1 1.00e+01 1.00e-02 8.28e+01 ... (remaining 16836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3561 0.060 - 0.119: 675 0.119 - 0.179: 74 0.179 - 0.239: 4 0.239 - 0.299: 3 Chirality restraints: 4317 Sorted by residual: chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 4314 not shown) Planarity restraints: 4752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 490 " 0.088 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO B 491 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 294 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO C 295 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 906 " -0.015 2.00e-02 2.50e+03 1.40e-02 3.41e+00 pdb=" CG PHE B 906 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 906 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 906 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 906 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 906 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 906 " -0.001 2.00e-02 2.50e+03 ... (remaining 4749 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 363 2.65 - 3.21: 24370 3.21 - 3.77: 37328 3.77 - 4.34: 50951 4.34 - 4.90: 84413 Nonbonded interactions: 197425 Sorted by model distance: nonbonded pdb=" OD1 ASP A 568 " pdb=" OG1 THR A 572 " model vdw 2.085 2.440 nonbonded pdb=" OD1 ASP B 568 " pdb=" OG1 THR B 572 " model vdw 2.105 2.440 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.150 2.440 nonbonded pdb=" OD1 ASP C 568 " pdb=" OG1 THR C 572 " model vdw 2.165 2.440 nonbonded pdb=" OE2 GLU A 725 " pdb=" NE2 HIS A1064 " model vdw 2.166 2.520 ... (remaining 197420 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.410 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 68.020 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 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 0.134 27090 Z= 0.294 Angle : 0.635 9.273 36891 Z= 0.329 Chirality : 0.047 0.299 4317 Planarity : 0.004 0.127 4710 Dihedral : 15.332 118.620 10587 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.15), residues: 3267 helix: 1.60 (0.22), residues: 612 sheet: -0.62 (0.20), residues: 672 loop : -1.83 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 886 HIS 0.003 0.001 HIS B 519 PHE 0.033 0.001 PHE B 906 TYR 0.017 0.001 TYR A 756 ARG 0.007 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3059 (mmp) cc_final: 0.2738 (mmp) REVERT: A 341 VAL cc_start: 0.8466 (t) cc_final: 0.8089 (p) REVERT: A 578 ASP cc_start: 0.6394 (t70) cc_final: 0.5085 (t70) REVERT: A 731 MET cc_start: 0.8960 (ptm) cc_final: 0.8689 (ptt) REVERT: B 353 TRP cc_start: 0.5672 (p-90) cc_final: 0.5026 (p-90) REVERT: C 585 LEU cc_start: 0.6251 (mt) cc_final: 0.5954 (mp) REVERT: C 780 GLU cc_start: 0.7435 (tt0) cc_final: 0.7221 (mt-10) REVERT: C 902 MET cc_start: 0.8970 (tpp) cc_final: 0.8705 (tpt) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.3844 time to fit residues: 248.7886 Evaluate side-chains 218 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 132 optimal weight: 30.0000 chunk 256 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 296 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 856 ASN B 544 ASN B 613 GLN B 787 GLN B 853 GLN B 955 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C1071 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 27090 Z= 0.377 Angle : 0.715 12.545 36891 Z= 0.365 Chirality : 0.051 0.317 4317 Planarity : 0.005 0.058 4710 Dihedral : 10.717 114.250 4725 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.68 % Allowed : 8.68 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.14), residues: 3267 helix: 1.25 (0.21), residues: 597 sheet: -0.71 (0.19), residues: 708 loop : -2.05 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 64 HIS 0.007 0.001 HIS C1058 PHE 0.031 0.002 PHE A 906 TYR 0.032 0.002 TYR C 265 ARG 0.012 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 215 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3263 (mmp) cc_final: 0.2918 (mmp) REVERT: A 731 MET cc_start: 0.8777 (ptm) cc_final: 0.8530 (ptt) REVERT: A 980 ILE cc_start: 0.8533 (mm) cc_final: 0.8248 (mt) REVERT: B 54 LEU cc_start: 0.8086 (mm) cc_final: 0.7683 (mm) REVERT: B 153 MET cc_start: 0.2569 (tpp) cc_final: 0.2320 (tpt) REVERT: B 353 TRP cc_start: 0.5552 (p-90) cc_final: 0.5134 (p-90) REVERT: B 436 TRP cc_start: 0.4969 (p90) cc_final: 0.4696 (p90) outliers start: 48 outliers final: 31 residues processed: 250 average time/residue: 0.3269 time to fit residues: 136.4801 Evaluate side-chains 219 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 297 optimal weight: 6.9990 chunk 321 optimal weight: 0.9990 chunk 264 optimal weight: 3.9990 chunk 295 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B 544 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27090 Z= 0.260 Angle : 0.589 9.457 36891 Z= 0.304 Chirality : 0.046 0.273 4317 Planarity : 0.004 0.053 4710 Dihedral : 9.077 99.945 4725 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.17 % Allowed : 10.96 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3267 helix: 1.55 (0.22), residues: 600 sheet: -0.72 (0.19), residues: 696 loop : -2.01 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.003 0.001 HIS C1058 PHE 0.019 0.001 PHE A 906 TYR 0.023 0.001 TYR C 265 ARG 0.007 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 193 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3260 (mmp) cc_final: 0.2869 (mmp) REVERT: A 878 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8143 (tt) REVERT: A 980 ILE cc_start: 0.8504 (mm) cc_final: 0.8164 (mt) REVERT: B 54 LEU cc_start: 0.8046 (mm) cc_final: 0.7631 (mm) REVERT: B 353 TRP cc_start: 0.5462 (p-90) cc_final: 0.5133 (p-90) REVERT: B 878 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8132 (tt) REVERT: C 54 LEU cc_start: 0.7375 (mt) cc_final: 0.7121 (mt) REVERT: C 177 MET cc_start: 0.2558 (pmm) cc_final: 0.1151 (mmp) REVERT: C 242 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5838 (mp) REVERT: C 981 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8860 (mm) outliers start: 62 outliers final: 35 residues processed: 243 average time/residue: 0.3308 time to fit residues: 136.1886 Evaluate side-chains 217 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 178 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 0.8980 chunk 223 optimal weight: 0.1980 chunk 154 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 141 optimal weight: 8.9990 chunk 199 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 chunk 316 optimal weight: 0.0370 chunk 155 optimal weight: 6.9990 chunk 282 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN B 544 ASN C 81 ASN C 239 GLN C1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 27090 Z= 0.156 Angle : 0.543 9.744 36891 Z= 0.276 Chirality : 0.045 0.320 4317 Planarity : 0.004 0.048 4710 Dihedral : 8.166 93.048 4725 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.14 % Allowed : 12.50 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3267 helix: 1.97 (0.22), residues: 594 sheet: -0.44 (0.20), residues: 669 loop : -1.91 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.002 0.000 HIS C 245 PHE 0.036 0.001 PHE A 342 TYR 0.026 0.001 TYR A 508 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 192 time to evaluate : 2.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3065 (mmp) cc_final: 0.2693 (mmp) REVERT: A 394 ASN cc_start: 0.6977 (OUTLIER) cc_final: 0.6458 (p0) REVERT: A 452 MET cc_start: 0.6153 (mmp) cc_final: 0.5687 (mmp) REVERT: A 878 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8130 (tt) REVERT: A 980 ILE cc_start: 0.8437 (mm) cc_final: 0.8163 (mt) REVERT: B 54 LEU cc_start: 0.7974 (mm) cc_final: 0.7599 (mm) REVERT: B 353 TRP cc_start: 0.5448 (p-90) cc_final: 0.5047 (p-90) REVERT: C 177 MET cc_start: 0.3014 (pmm) cc_final: 0.1626 (mmp) REVERT: C 220 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6416 (m-80) REVERT: C 242 LEU cc_start: 0.6038 (tp) cc_final: 0.5780 (mp) outliers start: 61 outliers final: 38 residues processed: 241 average time/residue: 0.3337 time to fit residues: 135.5000 Evaluate side-chains 214 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 173 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 3.9990 chunk 179 optimal weight: 0.2980 chunk 4 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 269 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 283 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS B 26 GLN B 185 ASN B 188 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1083 HIS C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.089 27090 Z= 0.625 Angle : 0.795 9.662 36891 Z= 0.415 Chirality : 0.053 0.433 4317 Planarity : 0.005 0.052 4710 Dihedral : 8.242 82.942 4725 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.17 % Favored : 91.80 % Rotamer: Outliers : 3.50 % Allowed : 13.45 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.14), residues: 3267 helix: 0.50 (0.20), residues: 651 sheet: -0.91 (0.20), residues: 648 loop : -2.17 (0.12), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 104 HIS 0.006 0.001 HIS C1088 PHE 0.042 0.003 PHE B 927 TYR 0.027 0.002 TYR A 904 ARG 0.007 0.001 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 180 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3606 (mmp) cc_final: 0.3217 (mmp) REVERT: A 265 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.6448 (t80) REVERT: A 878 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8107 (tt) REVERT: B 42 VAL cc_start: 0.8289 (p) cc_final: 0.8043 (m) REVERT: B 54 LEU cc_start: 0.7945 (mm) cc_final: 0.7472 (mm) REVERT: B 153 MET cc_start: 0.2282 (tpp) cc_final: 0.2049 (tpt) REVERT: B 878 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8199 (tt) REVERT: B 931 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8846 (tt) REVERT: C 177 MET cc_start: 0.2760 (pmm) cc_final: 0.1177 (mmp) REVERT: C 690 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.6774 (mm-40) REVERT: C 981 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8888 (mm) outliers start: 100 outliers final: 61 residues processed: 265 average time/residue: 0.3178 time to fit residues: 143.1800 Evaluate side-chains 229 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 162 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 106 optimal weight: 1.9990 chunk 284 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 316 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 173 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 949 GLN C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27090 Z= 0.178 Angle : 0.573 9.614 36891 Z= 0.293 Chirality : 0.046 0.361 4317 Planarity : 0.004 0.050 4710 Dihedral : 7.233 76.236 4725 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.24 % Allowed : 15.55 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3267 helix: 1.45 (0.21), residues: 618 sheet: -0.71 (0.19), residues: 714 loop : -2.01 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 633 HIS 0.002 0.000 HIS A1088 PHE 0.021 0.001 PHE A 371 TYR 0.017 0.001 TYR A 265 ARG 0.004 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 175 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3312 (mmp) cc_final: 0.3059 (mmp) REVERT: A 265 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.6195 (t80) REVERT: A 878 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8121 (tt) REVERT: B 42 VAL cc_start: 0.8292 (p) cc_final: 0.8055 (m) REVERT: B 54 LEU cc_start: 0.7867 (mm) cc_final: 0.7466 (mm) REVERT: B 153 MET cc_start: 0.2270 (tpp) cc_final: 0.2031 (tpt) REVERT: B 353 TRP cc_start: 0.5720 (p-90) cc_final: 0.5047 (p-90) REVERT: B 878 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8073 (tt) REVERT: B 918 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: C 177 MET cc_start: 0.3026 (pmm) cc_final: 0.1753 (mmp) REVERT: C 242 LEU cc_start: 0.6160 (tp) cc_final: 0.5891 (mp) REVERT: C 981 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8913 (mm) outliers start: 64 outliers final: 40 residues processed: 226 average time/residue: 0.3257 time to fit residues: 124.8395 Evaluate side-chains 208 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 163 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 180 optimal weight: 5.9990 chunk 231 optimal weight: 20.0000 chunk 179 optimal weight: 1.9990 chunk 266 optimal weight: 30.0000 chunk 176 optimal weight: 1.9990 chunk 315 optimal weight: 0.9980 chunk 197 optimal weight: 0.0970 chunk 192 optimal weight: 2.9990 chunk 145 optimal weight: 0.0980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 417 ASN A1048 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.096 27090 Z= 0.151 Angle : 0.541 9.609 36891 Z= 0.272 Chirality : 0.044 0.367 4317 Planarity : 0.004 0.051 4710 Dihedral : 6.421 67.766 4725 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.89 % Allowed : 16.46 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3267 helix: 1.83 (0.22), residues: 621 sheet: -0.61 (0.19), residues: 714 loop : -1.89 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.002 0.000 HIS B1083 PHE 0.016 0.001 PHE A 371 TYR 0.014 0.001 TYR A 265 ARG 0.003 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 188 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3271 (mmp) cc_final: 0.3057 (mmp) REVERT: A 265 TYR cc_start: 0.6662 (OUTLIER) cc_final: 0.5987 (t80) REVERT: A 904 TYR cc_start: 0.7873 (m-10) cc_final: 0.7671 (m-10) REVERT: B 42 VAL cc_start: 0.8325 (p) cc_final: 0.8082 (m) REVERT: B 54 LEU cc_start: 0.7811 (mm) cc_final: 0.7487 (mm) REVERT: B 153 MET cc_start: 0.2208 (tpp) cc_final: 0.1931 (tpt) REVERT: B 353 TRP cc_start: 0.5914 (p-90) cc_final: 0.5137 (p-90) REVERT: B 878 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8042 (tt) REVERT: C 177 MET cc_start: 0.2918 (pmm) cc_final: 0.1789 (mmm) REVERT: C 242 LEU cc_start: 0.6128 (tp) cc_final: 0.5850 (mp) REVERT: C 981 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8854 (mm) outliers start: 54 outliers final: 39 residues processed: 233 average time/residue: 0.3418 time to fit residues: 136.1839 Evaluate side-chains 221 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 2.9990 chunk 125 optimal weight: 0.0470 chunk 188 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 214 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 286 optimal weight: 0.7980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 394 ASN A 417 ASN B 544 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27090 Z= 0.170 Angle : 0.547 9.619 36891 Z= 0.274 Chirality : 0.044 0.373 4317 Planarity : 0.004 0.046 4710 Dihedral : 5.975 60.091 4725 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.00 % Allowed : 16.60 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3267 helix: 1.82 (0.22), residues: 639 sheet: -0.57 (0.19), residues: 714 loop : -1.87 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.004 0.000 HIS A1048 PHE 0.015 0.001 PHE A 429 TYR 0.018 0.001 TYR A1138 ARG 0.003 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 188 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.6648 (OUTLIER) cc_final: 0.6024 (t80) REVERT: B 42 VAL cc_start: 0.8279 (p) cc_final: 0.8024 (m) REVERT: B 54 LEU cc_start: 0.7796 (mm) cc_final: 0.7499 (mm) REVERT: B 153 MET cc_start: 0.2167 (tpp) cc_final: 0.1906 (tpt) REVERT: B 353 TRP cc_start: 0.5930 (p-90) cc_final: 0.5161 (p-90) REVERT: B 878 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8063 (tt) REVERT: C 177 MET cc_start: 0.2741 (pmm) cc_final: 0.1686 (mmm) REVERT: C 242 LEU cc_start: 0.6042 (tp) cc_final: 0.5773 (mp) REVERT: C 981 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8860 (mm) outliers start: 57 outliers final: 44 residues processed: 231 average time/residue: 0.3284 time to fit residues: 128.5009 Evaluate side-chains 228 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 181 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 chunk 293 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 127 optimal weight: 9.9990 chunk 230 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 265 optimal weight: 5.9990 chunk 277 optimal weight: 3.9990 chunk 292 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27090 Z= 0.184 Angle : 0.556 9.720 36891 Z= 0.279 Chirality : 0.044 0.362 4317 Planarity : 0.004 0.047 4710 Dihedral : 5.688 56.141 4725 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.82 % Allowed : 16.81 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3267 helix: 1.83 (0.22), residues: 639 sheet: -0.56 (0.19), residues: 714 loop : -1.84 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 64 HIS 0.003 0.000 HIS A 207 PHE 0.033 0.001 PHE C 86 TYR 0.023 0.001 TYR C 200 ARG 0.003 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 181 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.6710 (OUTLIER) cc_final: 0.6079 (t80) REVERT: B 42 VAL cc_start: 0.8379 (p) cc_final: 0.8135 (m) REVERT: B 54 LEU cc_start: 0.7774 (mm) cc_final: 0.7483 (mm) REVERT: B 153 MET cc_start: 0.2057 (tpp) cc_final: 0.1811 (tpt) REVERT: B 353 TRP cc_start: 0.5950 (p-90) cc_final: 0.5166 (p-90) REVERT: B 878 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8037 (tt) REVERT: C 242 LEU cc_start: 0.6024 (tp) cc_final: 0.5751 (mp) REVERT: C 981 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8864 (mm) outliers start: 52 outliers final: 43 residues processed: 222 average time/residue: 0.3255 time to fit residues: 123.8143 Evaluate side-chains 222 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 176 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 215 optimal weight: 0.0470 chunk 325 optimal weight: 6.9990 chunk 299 optimal weight: 0.7980 chunk 259 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 206 optimal weight: 0.0970 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 27090 Z= 0.149 Angle : 0.553 10.136 36891 Z= 0.276 Chirality : 0.044 0.353 4317 Planarity : 0.004 0.050 4710 Dihedral : 5.382 56.464 4725 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.65 % Allowed : 16.91 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3267 helix: 1.91 (0.22), residues: 642 sheet: -0.40 (0.19), residues: 711 loop : -1.80 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 64 HIS 0.003 0.000 HIS A1048 PHE 0.034 0.001 PHE C 86 TYR 0.026 0.001 TYR C 200 ARG 0.003 0.000 ARG C 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 186 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1869 (mmp) cc_final: 0.1462 (mmp) REVERT: A 265 TYR cc_start: 0.6748 (OUTLIER) cc_final: 0.6172 (t80) REVERT: B 42 VAL cc_start: 0.8378 (p) cc_final: 0.8128 (m) REVERT: B 54 LEU cc_start: 0.7739 (mm) cc_final: 0.7472 (mm) REVERT: B 153 MET cc_start: 0.2047 (tpp) cc_final: 0.1781 (tpt) REVERT: B 353 TRP cc_start: 0.5910 (p-90) cc_final: 0.5199 (p-90) REVERT: B 878 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8088 (tt) REVERT: C 42 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8878 (m) REVERT: C 242 LEU cc_start: 0.6062 (tp) cc_final: 0.5835 (mp) REVERT: C 981 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8855 (mm) outliers start: 47 outliers final: 37 residues processed: 222 average time/residue: 0.3223 time to fit residues: 121.6342 Evaluate side-chains 221 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 180 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 1.9990 chunk 79 optimal weight: 0.0570 chunk 239 optimal weight: 0.2980 chunk 38 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 259 optimal weight: 0.0980 chunk 108 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 228 optimal weight: 20.0000 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 658 ASN C 87 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.184150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118704 restraints weight = 42969.508| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.88 r_work: 0.3281 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27090 Z= 0.213 Angle : 0.576 10.336 36891 Z= 0.288 Chirality : 0.045 0.557 4317 Planarity : 0.004 0.049 4710 Dihedral : 5.448 56.323 4725 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.58 % Allowed : 17.26 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.14), residues: 3267 helix: 1.87 (0.22), residues: 639 sheet: -0.51 (0.19), residues: 717 loop : -1.80 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 64 HIS 0.003 0.001 HIS C1058 PHE 0.033 0.001 PHE C 86 TYR 0.024 0.001 TYR C 200 ARG 0.002 0.000 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5013.16 seconds wall clock time: 93 minutes 6.08 seconds (5586.08 seconds total)