Starting phenix.real_space_refine on Sun Sep 29 09:09:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l06_23095/09_2024/7l06_23095_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l06_23095/09_2024/7l06_23095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l06_23095/09_2024/7l06_23095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l06_23095/09_2024/7l06_23095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l06_23095/09_2024/7l06_23095_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l06_23095/09_2024/7l06_23095_neut_trim.cif" } resolution = 3.3 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= -0.002 sd= 0.047 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: 5 Type Number sf(0) Gaussians S 147 5.16 5 C 23369 2.51 5 N 6047 2.21 5 O 7309 1.98 5 H 35068 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 238 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 71940 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 15038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 15038 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "B" Number of atoms: 15038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 15038 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "C" Number of atoms: 15018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 15018 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "D" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3247 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain breaks: 1 Chain: "E" Number of atoms: 3228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3228 Classifications: {'peptide': 213} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "F" Number of atoms: 3198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3198 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "G" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3247 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain breaks: 1 Chain: "H" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3247 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain breaks: 1 Chain: "K" Number of atoms: 3228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3228 Classifications: {'peptide': 213} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "L" Number of atoms: 3198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3198 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "M" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3247 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain breaks: 1 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 3, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "S" 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: "T" 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: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" 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: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 3, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "Y" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 25.95, per 1000 atoms: 0.36 Number of scatterers: 71940 At special positions: 0 Unit cell: (186.208, 178.802, 213.716, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 147 16.00 O 7309 8.00 N 6047 7.00 C 23369 6.00 H 35068 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, 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=2.12 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.09 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.06 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=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=1.88 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.16 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.00 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=2.12 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.09 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.06 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=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=1.88 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.16 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.00 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=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.10 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.06 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=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.26 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 208 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.10 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.06 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.13 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.06 Simple disulfide: pdb=" SG CYS G 142 " - pdb=" SG CYS G 208 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.26 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 208 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.10 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.06 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.13 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.06 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 208 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-2 " MAN N 5 " - " MAN N 6 " " MAN X 5 " - " MAN X 6 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA J 3 " - " MAN J 5 " " BMA N 3 " - " MAN N 4 " " MAN N 4 " - " MAN N 5 " " BMA W 3 " - " MAN W 5 " " BMA X 3 " - " MAN X 4 " " MAN X 4 " - " MAN X 5 " BETA1-3 " BMA N 3 " - " BMA N 8 " " MAN N 4 " - " BMA N 7 " " BMA X 3 " - " BMA X 8 " " MAN X 4 " - " BMA X 7 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " BETA1-6 " BMA P 3 " - " BMA P 5 " " BMA U 3 " - " BMA U 5 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 616 " " NAG B1301 " - " ASN B 61 " " NAG B1303 " - " ASN B 343 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG C1201 " - " ASN C 657 " " NAG C1202 " - " ASN C1074 " " NAG C1203 " - " ASN C 61 " " NAG C1204 " - " ASN C 282 " " NAG C1205 " - " ASN C 331 " " NAG C1206 " - " ASN C 343 " " NAG C1207 " - " ASN C 603 " " NAG C1208 " - " ASN C 616 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A 801 " " NAG N 1 " - " ASN A 717 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A 709 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C1134 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN B1134 " " NAG W 1 " - " ASN B 801 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B1098 " Time building additional restraints: 13.89 Conformation dependent library (CDL) restraints added in 4.2 seconds 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8652 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 89 sheets defined 19.3% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.38 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.890A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.569A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.228A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 759 removed outlier: 6.975A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 4.198A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.901A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.577A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.580A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.537A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.588A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.800A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.890A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.569A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.230A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 759 removed outlier: 6.975A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 4.198A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.900A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.577A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.581A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.538A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.588A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.799A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.889A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.569A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.227A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 759 removed outlier: 6.975A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.806A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.798A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 52A through 55 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'D' and resid 196 through 199 removed outlier: 3.989A pdb=" N GLY D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 199' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.784A pdb=" N PHE E 83 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 127 removed outlier: 4.049A pdb=" N SER E 127 " --> pdb=" O GLU E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.503A pdb=" N PHE F 83 " --> pdb=" O PHE F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'F' and resid 183 through 187 Processing helix chain 'G' and resid 28 through 32 removed outlier: 4.057A pdb=" N ALA G 31 " --> pdb=" O ARG G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 52A through 55 removed outlier: 3.629A pdb=" N THR G 55 " --> pdb=" O THR G 52A" (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 52A through 55' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 163 through 165 No H-bonds generated for 'chain 'G' and resid 163 through 165' Processing helix chain 'G' and resid 196 through 199 removed outlier: 4.179A pdb=" N GLY G 199 " --> pdb=" O SER G 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 196 through 199' Processing helix chain 'H' and resid 52A through 55 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 196 through 199 removed outlier: 3.988A pdb=" N GLY H 199 " --> pdb=" O SER H 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 196 through 199' Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.784A pdb=" N PHE K 83 " --> pdb=" O PHE K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 127 removed outlier: 4.049A pdb=" N SER K 127 " --> pdb=" O GLU K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 187 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.502A pdb=" N PHE L 83 " --> pdb=" O PHE L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 187 Processing helix chain 'M' and resid 28 through 32 removed outlier: 4.058A pdb=" N ALA M 31 " --> pdb=" O ARG M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 52A through 55 removed outlier: 3.628A pdb=" N THR M 55 " --> pdb=" O THR M 52A" (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 52A through 55' Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 163 through 165 No H-bonds generated for 'chain 'M' and resid 163 through 165' Processing helix chain 'M' and resid 196 through 199 removed outlier: 4.180A pdb=" N GLY M 199 " --> pdb=" O SER M 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 196 through 199' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.221A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.249A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.210A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.728A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.529A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.268A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.540A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.123A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 453 removed outlier: 5.845A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.344A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.821A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1078 removed outlier: 4.469A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.499A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.220A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.210A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.729A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.529A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.269A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.539A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.124A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 448 through 453 removed outlier: 5.844A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.345A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 715 removed outlier: 4.469A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.821A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1081 through 1083 removed outlier: 4.500A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.007A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.366A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.728A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.530A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.240A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.121A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.725A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 448 through 453 removed outlier: 5.846A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.403A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.403A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.496A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.690A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.605A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N SER D 112 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL D 12 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 89 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.605A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N SER D 112 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL D 12 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.209A pdb=" N TYR D 185 " --> pdb=" O ASP D 146 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.209A pdb=" N TYR D 185 " --> pdb=" O ASP D 146 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 152 through 157 removed outlier: 3.865A pdb=" N TYR D 206 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.337A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS E 50 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.565A pdb=" N SER E 95 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 115 through 118 removed outlier: 4.302A pdb=" N ASN E 138 " --> pdb=" O TYR E 173 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER E 174 " --> pdb=" O THR E 164 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AG3, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.691A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.511A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 10 through 13 Processing sheet with id=AG6, first strand: chain 'F' and resid 114 through 118 removed outlier: 5.622A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AG8, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AG9, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.674A pdb=" N VAL G 12 " --> pdb=" O SER G 112 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET G 34 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.674A pdb=" N VAL G 12 " --> pdb=" O SER G 112 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 120 through 124 removed outlier: 6.148A pdb=" N TYR G 185 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 120 through 124 removed outlier: 6.148A pdb=" N TYR G 185 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 153 through 157 removed outlier: 4.279A pdb=" N TYR G 206 " --> pdb=" O VAL G 225 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AH6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.605A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N SER H 112 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE H 89 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.605A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N SER H 112 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.209A pdb=" N TYR H 185 " --> pdb=" O ASP H 146 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.209A pdb=" N TYR H 185 " --> pdb=" O ASP H 146 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 152 through 157 removed outlier: 3.865A pdb=" N TYR H 206 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AI3, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.337A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS K 50 " --> pdb=" O THR K 53 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.565A pdb=" N SER K 95 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 115 through 118 removed outlier: 4.303A pdb=" N ASN K 138 " --> pdb=" O TYR K 173 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER K 174 " --> pdb=" O THR K 164 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AI7, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.691A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.512A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AJ1, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.621A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AJ3, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AJ4, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.674A pdb=" N VAL M 12 " --> pdb=" O SER M 112 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N MET M 34 " --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.674A pdb=" N VAL M 12 " --> pdb=" O SER M 112 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'M' and resid 120 through 124 removed outlier: 6.148A pdb=" N TYR M 185 " --> pdb=" O ASP M 146 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'M' and resid 120 through 124 removed outlier: 6.148A pdb=" N TYR M 185 " --> pdb=" O ASP M 146 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'M' and resid 153 through 157 removed outlier: 4.280A pdb=" N TYR M 206 " --> pdb=" O VAL M 225 " (cutoff:3.500A) 1656 hydrogen bonds defined for protein. 4446 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: 34.96 Time building geometry restraints manager: 17.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 35065 1.04 - 1.25: 5787 1.25 - 1.46: 12505 1.46 - 1.66: 19196 1.66 - 1.87: 187 Bond restraints: 72740 Sorted by residual: bond pdb=" C ILE B1081 " pdb=" O ILE B1081 " ideal model delta sigma weight residual 1.236 1.164 0.072 9.90e-03 1.02e+04 5.32e+01 bond pdb=" C ILE A1081 " pdb=" O ILE A1081 " ideal model delta sigma weight residual 1.236 1.165 0.071 9.90e-03 1.02e+04 5.16e+01 bond pdb=" C VAL H 144 " pdb=" O VAL H 144 " ideal model delta sigma weight residual 1.238 1.170 0.067 1.17e-02 7.31e+03 3.32e+01 bond pdb=" NE ARG A 454 " pdb=" CZ ARG A 454 " ideal model delta sigma weight residual 1.326 1.389 -0.063 1.10e-02 8.26e+03 3.26e+01 bond pdb=" C VAL D 144 " pdb=" O VAL D 144 " ideal model delta sigma weight residual 1.238 1.171 0.067 1.17e-02 7.31e+03 3.23e+01 ... (remaining 72735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.53: 130607 9.53 - 19.05: 30 19.05 - 28.58: 17 28.58 - 38.11: 3 38.11 - 47.64: 8 Bond angle restraints: 130665 Sorted by residual: angle pdb="HD21 ASN B 709 " pdb=" ND2 ASN B 709 " pdb="HD22 ASN B 709 " ideal model delta sigma weight residual 120.00 72.36 47.64 3.00e+00 1.11e-01 2.52e+02 angle pdb="HD21 ASN A1098 " pdb=" ND2 ASN A1098 " pdb="HD22 ASN A1098 " ideal model delta sigma weight residual 120.00 73.30 46.70 3.00e+00 1.11e-01 2.42e+02 angle pdb="HD21 ASN B1098 " pdb=" ND2 ASN B1098 " pdb="HD22 ASN B1098 " ideal model delta sigma weight residual 120.00 73.33 46.67 3.00e+00 1.11e-01 2.42e+02 angle pdb="HD21 ASN B 616 " pdb=" ND2 ASN B 616 " pdb="HD22 ASN B 616 " ideal model delta sigma weight residual 120.00 73.70 46.30 3.00e+00 1.11e-01 2.38e+02 angle pdb=" CG ASN B 709 " pdb=" ND2 ASN B 709 " pdb="HD22 ASN B 709 " ideal model delta sigma weight residual 120.00 74.53 45.47 3.00e+00 1.11e-01 2.30e+02 ... (remaining 130660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.28: 33986 22.28 - 44.56: 1333 44.56 - 66.84: 435 66.84 - 89.12: 166 89.12 - 111.40: 51 Dihedral angle restraints: 35971 sinusoidal: 19977 harmonic: 15994 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -173.00 87.00 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " pdb=" CB CYS E 88 " ideal model delta sinusoidal sigma weight residual -86.00 -0.23 -85.77 1 1.00e+01 1.00e-02 8.89e+01 dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual -86.00 -0.25 -85.75 1 1.00e+01 1.00e-02 8.89e+01 ... (remaining 35968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.811: 6077 0.811 - 1.622: 3 1.622 - 2.433: 4 2.433 - 3.244: 1 3.244 - 4.055: 3 Chirality restraints: 6088 Sorted by residual: chirality pdb=" C1 MAN P 4 " pdb=" O3 BMA P 3 " pdb=" C2 MAN P 4 " pdb=" O5 MAN P 4 " both_signs ideal model delta sigma weight residual False 2.40 1.84 0.56 2.00e-02 2.50e+03 7.84e+02 chirality pdb=" C1 BMA P 3 " pdb=" O4 NAG P 2 " pdb=" C2 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-02 2.50e+03 4.13e+02 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 1.65 -4.05 2.00e-01 2.50e+01 4.11e+02 ... (remaining 6085 not shown) Planarity restraints: 10857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.182 2.00e-02 2.50e+03 3.85e-01 2.22e+03 pdb=" CG ASN A 709 " 0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " 0.085 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.163 2.00e-02 2.50e+03 pdb="HD21 ASN A 709 " 0.547 2.00e-02 2.50e+03 pdb="HD22 ASN A 709 " -0.716 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " 0.184 2.00e-02 2.50e+03 3.85e-01 2.22e+03 pdb=" CG ASN A 801 " -0.114 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " -0.082 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " -0.170 2.00e-02 2.50e+03 pdb="HD21 ASN A 801 " -0.537 2.00e-02 2.50e+03 pdb="HD22 ASN A 801 " 0.719 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 717 " 0.177 2.00e-02 2.50e+03 3.85e-01 2.22e+03 pdb=" CG ASN A 717 " -0.110 2.00e-02 2.50e+03 pdb=" OD1 ASN A 717 " -0.088 2.00e-02 2.50e+03 pdb=" ND2 ASN A 717 " -0.161 2.00e-02 2.50e+03 pdb="HD21 ASN A 717 " -0.539 2.00e-02 2.50e+03 pdb="HD22 ASN A 717 " 0.721 2.00e-02 2.50e+03 ... (remaining 10854 not shown) Histogram of nonbonded interaction distances: 0.48 - 1.30: 9 1.30 - 2.13: 1790 2.13 - 2.95: 190044 2.95 - 3.78: 297674 3.78 - 4.60: 517163 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1006680 Sorted by model distance: nonbonded pdb=" OD2 ASP D 72 " pdb="HH12 ARG G 57 " model vdw 0.480 2.450 nonbonded pdb=" OD1 ASP D 72 " pdb="HH22 ARG G 57 " model vdw 1.027 2.450 nonbonded pdb="HH12 ARG H 57 " pdb=" OD2 ASP M 72 " model vdw 1.066 2.450 nonbonded pdb=" OD2 ASP H 72 " pdb="HH12 ARG M 57 " model vdw 1.090 2.450 nonbonded pdb="HD11 LEU H 45 " pdb=" HG2 PRO L 44 " model vdw 1.098 2.440 ... (remaining 1006675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 69 or (resid 80 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 \ or name HB3)) or resid 81 through 121 or (resid 122 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name ND2 or name H or name \ HA or name HB2 or name HB3 or name HD21)) or resid 123 through 143 or (resid 165 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name ND2 or name HA or name HB2 or name HB3 or name HD21)) or resid 166 through \ 172 or (resid 186 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or nam \ e HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ )) \ or resid 187 through 233 or (resid 234 and (name N or name CA or name C or name \ O or name CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 \ or name HB3 or name HD21)) or resid 235 through 245 or (resid 263 and (name N o \ r name CA or name C or name O or name CB or name HA or name HB1 or name HB2 or n \ ame HB3)) or resid 264 through 330 or (resid 331 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA o \ r name HB2 or name HB3 or name HD21)) or resid 332 through 342 or (resid 343 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or nam \ e ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 344 t \ hrough 444 or (resid 447 and (name N or name CA or name C or name O or name HA2 \ or name HA3)) or resid 448 through 454 or (resid 462 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or nam \ e HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 463 through 468 \ or (resid 489 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name \ HH )) or resid 490 through 501 or (resid 503 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 o \ r name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 504 t \ hrough 602 or (resid 603 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 o \ r name HD21)) or resid 604 through 615 or (resid 616 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name ND2 or name H or name \ HA or name HB2 or name HB3 or name HD21)) or resid 617 through 620 or (resid 641 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name ND2 or name HA or name HB2 or name HB3 or name HD21 or name HD22)) or resi \ d 642 through 656 or (resid 657 and (name N or name CA or name C or name O or na \ me CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or nam \ e HB3 or name HD21)) or resid 658 through 676 or (resid 689 and (name N or name \ CA or name C or name O or name CB or name OG or name HA or name HB2 or name HB3 \ or name HG )) or resid 690 through 716 or (resid 717 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name ND2 or name H or name \ HA or name HB2 or name HB3 or name HD21)) or resid 718 through 800 or (resid 801 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 8 \ 02 through 827 or (resid 854 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or nam \ e HZ1 or name HZ2 or name HZ3)) or resid 855 through 1097 or (resid 1098 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name ND \ 2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 1099 thro \ ugh 1147 or resid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 69 or (resid 80 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 \ or name HB3)) or resid 81 through 121 or (resid 122 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name ND2 or name H or name \ HA or name HB2 or name HB3 or name HD21)) or resid 123 through 143 or (resid 165 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name ND2 or name HA or name HB2 or name HB3 or name HD21)) or resid 166 through \ 172 or (resid 186 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or nam \ e HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ )) \ or resid 187 through 233 or (resid 234 and (name N or name CA or name C or name \ O or name CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 \ or name HB3 or name HD21)) or resid 235 through 245 or (resid 263 and (name N o \ r name CA or name C or name O or name CB or name HA or name HB1 or name HB2 or n \ ame HB3)) or resid 264 through 330 or (resid 331 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA o \ r name HB2 or name HB3 or name HD21)) or resid 332 through 342 or (resid 343 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or nam \ e ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 344 t \ hrough 444 or (resid 447 and (name N or name CA or name C or name O or name HA2 \ or name HA3)) or resid 448 through 454 or (resid 462 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or nam \ e HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 463 through 468 \ or (resid 489 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name \ HH )) or resid 490 through 501 or (resid 503 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 o \ r name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 504 t \ hrough 602 or (resid 603 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 o \ r name HD21)) or resid 604 through 615 or (resid 616 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name ND2 or name H or name \ HA or name HB2 or name HB3 or name HD21)) or resid 617 through 620 or (resid 641 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name ND2 or name HA or name HB2 or name HB3 or name HD21 or name HD22)) or resi \ d 642 through 656 or (resid 657 and (name N or name CA or name C or name O or na \ me CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or nam \ e HB3 or name HD21)) or resid 658 through 676 or (resid 689 and (name N or name \ CA or name C or name O or name CB or name OG or name HA or name HB2 or name HB3 \ or name HG )) or resid 690 through 716 or (resid 717 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name ND2 or name H or name \ HA or name HB2 or name HB3 or name HD21)) or resid 718 through 800 or (resid 801 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 8 \ 02 through 827 or (resid 854 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or nam \ e HZ1 or name HZ2 or name HZ3)) or resid 855 through 1097 or (resid 1098 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name ND \ 2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 1099 thro \ ugh 1147 or resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA o \ r name HB2 or name HB3)) or resid 62 through 1133 or (resid 1134 and (name N or \ name CA or name C or name O or name CB or name CG or name OD1 or name ND2 or nam \ e H or name HA or name HB2 or name HB3)) or resid 1135 through 1147 or resid 120 \ 1 through 1208)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'M' } ncs_group { reference = (chain 'E' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23)) or resid 3 through 212)) selection = chain 'F' selection = (chain 'K' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23)) or resid 3 through 212)) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = (chain 'J' and resid 1 through 4) selection = (chain 'P' and resid 1 through 4) selection = (chain 'U' and resid 1 through 4) selection = (chain 'W' and resid 1 through 4) } ncs_group { reference = chain 'N' selection = chain 'X' } 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: 1.640 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: 1.000 Extract box with map and model: 2.090 Check model and map are aligned: 0.410 Set scattering table: 0.550 Process input model: 126.110 Find NCS groups from input model: 2.560 Set up NCS constraints: 0.410 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: 0.020 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 : 0.014 0.113 37672 Z= 0.909 Angle : 1.654 19.519 51237 Z= 1.122 Chirality : 0.148 4.055 6088 Planarity : 0.015 0.290 6466 Dihedral : 14.802 111.399 14636 Min Nonbonded Distance : 1.245 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.87 % Allowed : 3.13 % Favored : 96.00 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.12), residues: 4540 helix: -1.06 (0.16), residues: 739 sheet: -0.01 (0.14), residues: 1298 loop : -0.28 (0.12), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.152 0.016 TRP D 157 HIS 0.014 0.003 HIS B1088 PHE 0.078 0.008 PHE A 220 TYR 0.158 0.011 TYR B 37 ARG 0.012 0.001 ARG F 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 495 time to evaluate : 4.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 ASN cc_start: 0.9049 (t0) cc_final: 0.8742 (t0) REVERT: B 62 VAL cc_start: 0.7520 (m) cc_final: 0.7221 (t) REVERT: C 426 PRO cc_start: 0.7263 (Cg_exo) cc_final: 0.6437 (Cg_endo) REVERT: C 987 PRO cc_start: 0.7740 (Cg_exo) cc_final: 0.7121 (Cg_endo) REVERT: F 14 SER cc_start: 0.8556 (m) cc_final: 0.8140 (p) REVERT: F 161 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6255 (mm-30) outliers start: 35 outliers final: 13 residues processed: 528 average time/residue: 1.2079 time to fit residues: 967.5299 Evaluate side-chains 281 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 268 time to evaluate : 4.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain M residue 187 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 387 optimal weight: 3.9990 chunk 347 optimal weight: 20.0000 chunk 193 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 359 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 chunk 267 optimal weight: 0.6980 chunk 416 optimal weight: 4.9990 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 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 234 ASN A 360 ASN A 779 GLN A 784 GLN A 925 ASN B 234 ASN B 317 ASN B 603 ASN B1002 GLN C 764 ASN C 804 GLN C 935 GLN C1005 GLN D 32 HIS H 32 HIS K 38 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 37672 Z= 0.222 Angle : 0.676 9.339 51237 Z= 0.358 Chirality : 0.050 0.806 6088 Planarity : 0.005 0.090 6466 Dihedral : 10.749 79.851 6525 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.98 % Favored : 97.97 % Rotamer: Outliers : 0.77 % Allowed : 6.66 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.12), residues: 4540 helix: 0.39 (0.18), residues: 729 sheet: 0.02 (0.13), residues: 1461 loop : -0.11 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 157 HIS 0.009 0.001 HIS D 32 PHE 0.021 0.001 PHE A 32 TYR 0.023 0.002 TYR A1067 ARG 0.025 0.001 ARG G 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 287 time to evaluate : 4.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 ASN cc_start: 0.9089 (t0) cc_final: 0.8733 (t0) REVERT: C 366 SER cc_start: 0.9044 (m) cc_final: 0.8653 (p) REVERT: F 14 SER cc_start: 0.8522 (m) cc_final: 0.8171 (p) REVERT: F 161 GLU cc_start: 0.6622 (mt-10) cc_final: 0.6104 (mm-30) REVERT: H 34 MET cc_start: 0.8526 (mmm) cc_final: 0.8293 (mmt) REVERT: K 161 GLU cc_start: 0.8201 (pm20) cc_final: 0.7874 (tm-30) REVERT: M 53 SER cc_start: 0.9030 (m) cc_final: 0.8819 (p) outliers start: 31 outliers final: 20 residues processed: 310 average time/residue: 1.1819 time to fit residues: 559.3348 Evaluate side-chains 251 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 231 time to evaluate : 4.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain K residue 70 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 231 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 346 optimal weight: 30.0000 chunk 283 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 417 optimal weight: 10.0000 chunk 451 optimal weight: 40.0000 chunk 371 optimal weight: 20.0000 chunk 414 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 334 optimal weight: 40.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 607 GLN A 644 GLN A 762 GLN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1002 GLN A1106 GLN B 66 HIS B 207 HIS B 641 ASN B 804 GLN B 901 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN B 926 GLN B 935 GLN B1005 GLN B1088 HIS B1113 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN G 35 ASN K 6 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.233 37672 Z= 0.716 Angle : 0.884 11.762 51237 Z= 0.466 Chirality : 0.056 0.812 6088 Planarity : 0.006 0.081 6466 Dihedral : 9.118 72.863 6509 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.82 % Favored : 95.11 % Rotamer: Outliers : 1.64 % Allowed : 8.05 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.22 (0.12), residues: 4540 helix: -0.83 (0.17), residues: 742 sheet: -0.57 (0.13), residues: 1439 loop : -0.85 (0.12), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B1102 HIS 0.011 0.002 HIS C1058 PHE 0.057 0.003 PHE C1089 TYR 0.037 0.003 TYR A1067 ARG 0.008 0.001 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 239 time to evaluate : 4.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: B 135 PHE cc_start: 0.5363 (m-80) cc_final: 0.5064 (m-80) REVERT: C 366 SER cc_start: 0.9171 (m) cc_final: 0.8889 (p) REVERT: C 451 TYR cc_start: 0.6417 (m-80) cc_final: 0.6035 (m-80) REVERT: C 516 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6176 (mp0) REVERT: E 60 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8794 (t) REVERT: F 161 GLU cc_start: 0.6538 (mt-10) cc_final: 0.5890 (mm-30) REVERT: H 148 PHE cc_start: 0.8769 (t80) cc_final: 0.8474 (t80) REVERT: M 26 ASN cc_start: 0.7275 (t0) cc_final: 0.6886 (t0) outliers start: 66 outliers final: 45 residues processed: 295 average time/residue: 1.1203 time to fit residues: 517.8451 Evaluate side-chains 247 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 199 time to evaluate : 4.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain K residue 32 TRP Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 210 ASN Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 211 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 412 optimal weight: 1.9990 chunk 313 optimal weight: 30.0000 chunk 216 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 199 optimal weight: 10.0000 chunk 280 optimal weight: 0.9980 chunk 419 optimal weight: 20.0000 chunk 443 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 397 optimal weight: 30.0000 chunk 119 optimal weight: 0.4980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A1011 GLN A1106 GLN B 901 GLN B 914 ASN C 66 HIS C 422 ASN K 6 GLN K 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 37672 Z= 0.218 Angle : 0.587 9.267 51237 Z= 0.309 Chirality : 0.047 0.742 6088 Planarity : 0.004 0.073 6466 Dihedral : 7.600 59.568 6509 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.14 % Allowed : 8.77 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.12), residues: 4540 helix: 0.21 (0.18), residues: 762 sheet: -0.41 (0.14), residues: 1460 loop : -0.55 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 47 HIS 0.004 0.001 HIS C1048 PHE 0.024 0.001 PHE C1089 TYR 0.018 0.001 TYR A1067 ARG 0.005 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 212 time to evaluate : 4.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 ASN cc_start: 0.9230 (t0) cc_final: 0.8924 (t0) REVERT: B 135 PHE cc_start: 0.5297 (m-80) cc_final: 0.4997 (m-80) REVERT: E 70 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: H 82 MET cc_start: 0.7320 (mpp) cc_final: 0.6984 (mpp) REVERT: H 148 PHE cc_start: 0.8725 (t80) cc_final: 0.8412 (t80) REVERT: L 24 ARG cc_start: 0.8517 (mpp80) cc_final: 0.7881 (mpp80) REVERT: M 26 ASN cc_start: 0.7217 (t0) cc_final: 0.6855 (t0) outliers start: 46 outliers final: 39 residues processed: 250 average time/residue: 1.0664 time to fit residues: 414.6922 Evaluate side-chains 235 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 195 time to evaluate : 4.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 210 ASN Chi-restraints excluded: chain L residue 123 GLU Chi-restraints excluded: chain L residue 210 ASN Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 148 PHE Chi-restraints excluded: chain M residue 211 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 369 optimal weight: 7.9990 chunk 251 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 330 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 378 optimal weight: 10.0000 chunk 306 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 chunk 398 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN G 35 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN M 26 ASN M 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.140 37672 Z= 0.426 Angle : 0.636 8.781 51237 Z= 0.334 Chirality : 0.048 0.752 6088 Planarity : 0.004 0.067 6466 Dihedral : 7.277 58.042 6509 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.44 % Allowed : 9.17 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.12), residues: 4540 helix: 0.12 (0.18), residues: 762 sheet: -0.58 (0.13), residues: 1480 loop : -0.73 (0.13), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1102 HIS 0.005 0.001 HIS C1101 PHE 0.037 0.002 PHE C1089 TYR 0.026 0.002 TYR A1067 ARG 0.004 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 205 time to evaluate : 4.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.7622 (m-80) REVERT: A 387 LEU cc_start: 0.9157 (mp) cc_final: 0.8896 (mp) REVERT: A 532 ASN cc_start: 0.9258 (t0) cc_final: 0.8956 (t0) REVERT: B 135 PHE cc_start: 0.5536 (m-80) cc_final: 0.5166 (m-80) REVERT: B 204 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.7166 (m-80) REVERT: B 392 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6966 (m-80) REVERT: B 1119 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7127 (m110) REVERT: C 740 MET cc_start: 0.7481 (mmm) cc_final: 0.7263 (mmm) REVERT: D 3 GLN cc_start: 0.7090 (tm-30) cc_final: 0.6862 (tm-30) REVERT: E 70 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: H 148 PHE cc_start: 0.8786 (t80) cc_final: 0.8483 (t80) REVERT: L 24 ARG cc_start: 0.8527 (mpp80) cc_final: 0.7962 (mpp80) REVERT: M 26 ASN cc_start: 0.7231 (t0) cc_final: 0.6875 (t0) outliers start: 58 outliers final: 42 residues processed: 252 average time/residue: 1.0714 time to fit residues: 422.1728 Evaluate side-chains 242 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 195 time to evaluate : 4.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 210 ASN Chi-restraints excluded: chain L residue 210 ASN Chi-restraints excluded: chain M residue 211 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 149 optimal weight: 0.8980 chunk 399 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 444 optimal weight: 4.9990 chunk 368 optimal weight: 40.0000 chunk 205 optimal weight: 30.0000 chunk 36 optimal weight: 30.0000 chunk 146 optimal weight: 0.9980 chunk 233 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 37672 Z= 0.234 Angle : 0.550 8.603 51237 Z= 0.288 Chirality : 0.046 0.732 6088 Planarity : 0.004 0.070 6466 Dihedral : 6.622 55.966 6508 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.09 % Allowed : 9.62 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.12), residues: 4540 helix: 0.68 (0.19), residues: 747 sheet: -0.53 (0.13), residues: 1465 loop : -0.54 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 47 HIS 0.003 0.001 HIS C1048 PHE 0.018 0.001 PHE C1089 TYR 0.018 0.001 TYR A1067 ARG 0.004 0.000 ARG G 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 198 time to evaluate : 4.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.9111 (mp) cc_final: 0.8873 (mp) REVERT: A 532 ASN cc_start: 0.9233 (t0) cc_final: 0.8850 (t0) REVERT: B 135 PHE cc_start: 0.5326 (m-80) cc_final: 0.4958 (m-80) REVERT: B 204 TYR cc_start: 0.7648 (OUTLIER) cc_final: 0.7324 (m-80) REVERT: B 392 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.6891 (m-80) REVERT: B 451 TYR cc_start: 0.5027 (m-80) cc_final: 0.4768 (m-80) REVERT: E 70 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: F 4 MET cc_start: 0.1877 (mpp) cc_final: 0.1520 (mpp) REVERT: H 148 PHE cc_start: 0.8768 (t80) cc_final: 0.8469 (t80) outliers start: 44 outliers final: 38 residues processed: 231 average time/residue: 1.1023 time to fit residues: 397.0659 Evaluate side-chains 235 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 4.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 210 ASN Chi-restraints excluded: chain L residue 210 ASN Chi-restraints excluded: chain M residue 211 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 428 optimal weight: 30.0000 chunk 50 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 324 optimal weight: 20.0000 chunk 251 optimal weight: 1.9990 chunk 373 optimal weight: 30.0000 chunk 247 optimal weight: 3.9990 chunk 442 optimal weight: 8.9990 chunk 276 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 chunk 204 optimal weight: 30.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 GLN C 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 37672 Z= 0.253 Angle : 0.535 8.190 51237 Z= 0.280 Chirality : 0.046 0.732 6088 Planarity : 0.004 0.070 6466 Dihedral : 6.244 55.011 6508 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.22 % Allowed : 9.79 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.12), residues: 4540 helix: 0.87 (0.19), residues: 747 sheet: -0.47 (0.13), residues: 1449 loop : -0.55 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 47 HIS 0.003 0.001 HIS H 212 PHE 0.020 0.001 PHE C1089 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG G 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 199 time to evaluate : 4.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.9090 (mp) cc_final: 0.8878 (mp) REVERT: A 532 ASN cc_start: 0.9211 (t0) cc_final: 0.8825 (t0) REVERT: B 204 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: B 392 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.6977 (m-80) REVERT: E 70 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: H 148 PHE cc_start: 0.8786 (t80) cc_final: 0.8489 (t80) REVERT: L 24 ARG cc_start: 0.8565 (mpp80) cc_final: 0.7992 (mpp80) outliers start: 49 outliers final: 41 residues processed: 239 average time/residue: 1.1196 time to fit residues: 417.9929 Evaluate side-chains 232 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 188 time to evaluate : 5.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 210 ASN Chi-restraints excluded: chain L residue 210 ASN Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 211 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 273 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 281 optimal weight: 0.9990 chunk 301 optimal weight: 8.9990 chunk 218 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 347 optimal weight: 30.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 37672 Z= 0.230 Angle : 0.527 7.810 51237 Z= 0.276 Chirality : 0.046 0.728 6088 Planarity : 0.004 0.072 6466 Dihedral : 6.029 54.807 6507 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.17 % Allowed : 9.94 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 4540 helix: 0.99 (0.19), residues: 744 sheet: -0.38 (0.14), residues: 1419 loop : -0.58 (0.13), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 47 HIS 0.003 0.001 HIS H 212 PHE 0.020 0.001 PHE D 148 TYR 0.018 0.001 TYR A1067 ARG 0.006 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 190 time to evaluate : 4.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 ASN cc_start: 0.9198 (t0) cc_final: 0.8808 (t0) REVERT: B 204 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: B 392 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7144 (m-80) REVERT: C 985 ASP cc_start: 0.8240 (p0) cc_final: 0.7789 (p0) REVERT: E 70 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: H 148 PHE cc_start: 0.8790 (t80) cc_final: 0.8503 (t80) outliers start: 47 outliers final: 40 residues processed: 228 average time/residue: 1.0679 time to fit residues: 385.5737 Evaluate side-chains 226 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 183 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 210 ASN Chi-restraints excluded: chain L residue 210 ASN Chi-restraints excluded: chain M residue 211 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 402 optimal weight: 20.0000 chunk 423 optimal weight: 30.0000 chunk 386 optimal weight: 10.0000 chunk 412 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 372 optimal weight: 1.9990 chunk 389 optimal weight: 40.0000 chunk 410 optimal weight: 10.0000 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 37672 Z= 0.376 Angle : 0.581 7.900 51237 Z= 0.304 Chirality : 0.047 0.739 6088 Planarity : 0.004 0.074 6466 Dihedral : 6.396 55.672 6507 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.17 % Allowed : 9.99 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.12), residues: 4540 helix: 0.63 (0.19), residues: 762 sheet: -0.53 (0.13), residues: 1417 loop : -0.72 (0.13), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1102 HIS 0.005 0.001 HIS C1101 PHE 0.030 0.001 PHE C1089 TYR 0.025 0.002 TYR A1067 ARG 0.004 0.000 ARG G 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 188 time to evaluate : 4.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: A 532 ASN cc_start: 0.9195 (t0) cc_final: 0.8835 (t0) REVERT: B 204 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: B 392 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: E 70 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: H 148 PHE cc_start: 0.8839 (t80) cc_final: 0.8552 (t80) REVERT: L 86 TYR cc_start: 0.7998 (m-80) cc_final: 0.7761 (m-10) outliers start: 47 outliers final: 43 residues processed: 226 average time/residue: 1.0724 time to fit residues: 380.3521 Evaluate side-chains 232 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 185 time to evaluate : 4.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 210 ASN Chi-restraints excluded: chain L residue 210 ASN Chi-restraints excluded: chain M residue 211 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 270 optimal weight: 9.9990 chunk 435 optimal weight: 9.9990 chunk 266 optimal weight: 0.5980 chunk 206 optimal weight: 2.9990 chunk 303 optimal weight: 20.0000 chunk 457 optimal weight: 30.0000 chunk 420 optimal weight: 30.0000 chunk 364 optimal weight: 5.9990 chunk 37 optimal weight: 0.0370 chunk 281 optimal weight: 0.6980 chunk 223 optimal weight: 10.0000 overall best weight: 2.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 37672 Z= 0.202 Angle : 0.514 7.740 51237 Z= 0.269 Chirality : 0.046 0.723 6088 Planarity : 0.004 0.073 6466 Dihedral : 5.964 53.924 6507 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.94 % Allowed : 10.21 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.12), residues: 4540 helix: 0.99 (0.19), residues: 765 sheet: -0.39 (0.14), residues: 1402 loop : -0.61 (0.13), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 47 HIS 0.003 0.001 HIS H 212 PHE 0.016 0.001 PHE D 148 TYR 0.016 0.001 TYR C1067 ARG 0.004 0.000 ARG G 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 4.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: A 532 ASN cc_start: 0.9166 (t0) cc_final: 0.8767 (t0) REVERT: B 204 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: B 392 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7440 (m-80) REVERT: E 70 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: H 148 PHE cc_start: 0.8825 (t80) cc_final: 0.8533 (t80) outliers start: 38 outliers final: 34 residues processed: 220 average time/residue: 1.0820 time to fit residues: 372.5868 Evaluate side-chains 220 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 182 time to evaluate : 4.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 210 ASN Chi-restraints excluded: chain M residue 211 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 289 optimal weight: 0.0570 chunk 387 optimal weight: 10.0000 chunk 111 optimal weight: 0.2980 chunk 335 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 364 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 374 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.6704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.110777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.067743 restraints weight = 367914.149| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.46 r_work: 0.3460 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 37672 Z= 0.259 Angle : 0.525 7.509 51237 Z= 0.274 Chirality : 0.045 0.729 6088 Planarity : 0.004 0.070 6466 Dihedral : 5.932 54.849 6507 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.07 % Allowed : 10.09 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.12), residues: 4540 helix: 1.02 (0.19), residues: 765 sheet: -0.41 (0.14), residues: 1411 loop : -0.61 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS H 212 PHE 0.018 0.001 PHE C1089 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG G 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13967.91 seconds wall clock time: 239 minutes 48.31 seconds (14388.31 seconds total)